Files on Internal Drive Unavailable after Indexing

Hello,

I am starting to have issues with version 2017.1 where when the project has completed indexing, the files are unavailable and the connection to my 2nd internal drive is lost. I can only get this back by restarting my PC (Windows 10). 

My setup is the program is on C:\ and the project files are on D:\.

Once this issue happens, I can no longer access the D:\ from anywhere, even the windows file explorer.

Below is a snippet from the log file. If more is needed, I can post more. 

Thanks for any help!

2017-03-28 13:54:44,364 [ 0] INFO - #com.intellij.idea.Main - ------------------------------------------------------ IDE STARTED ------------------------------------------------------ 
2017-03-28 13:54:44,661 [ 297] INFO - #com.intellij.util.ui.JBUI - UI scale factor: 1.0 
2017-03-28 13:54:44,708 [ 344] INFO - #com.intellij.idea.Main - IDE: PhpStorm (build #PS-171.3780.104, 21 Mar 2017 08:44) 
2017-03-28 13:54:44,708 [ 344] INFO - #com.intellij.idea.Main - OS: Windows 10 (10.0, x86) 
2017-03-28 13:54:44,708 [ 344] INFO - #com.intellij.idea.Main - JRE: 1.8.0_112-release-736-b13 (JetBrains s.r.o) 
2017-03-28 13:54:44,708 [ 344] INFO - #com.intellij.idea.Main - JVM: 25.112-b13 (OpenJDK Server VM) 
2017-03-28 13:54:44,755 [ 391] INFO - #com.intellij.idea.Main - JVM Args: -Xms128m -Xmx512m -XX:ReservedCodeCacheSize=240m -XX:+UseConcMarkSweepGC -XX:SoftRefLRUPolicyMSPerMB=50 -ea -Dsun.io.useCanonCaches=false -Djava.net.preferIPv4Stack=true -XX:+HeapDumpOnOutOfMemoryError -XX:-OmitStackTraceInFastThrow -Djb.vmOptionsFile=C:\Program Files (x86)\JetBrains\PhpStorm 2016.3\bin\phpstorm.exe.vmoptions -Xbootclasspath/a:C:\Program Files (x86)\JetBrains\PhpStorm 2016.3\lib\boot.jar -Didea.platform.prefix=PhpStorm -Didea.jre.check=true -Didea.paths.selector=PhpStorm2017.1 -XX:ErrorFile=C:\Users\Keith Andrews\java_error_in_phpstorm_%p.log -XX:HeapDumpPath=C:\Users\Keith Andrews\java_error_in_phpstorm.hprof 
2017-03-28 13:54:44,755 [ 391] INFO - #com.intellij.idea.Main - ext: C:\Program Files (x86)\JetBrains\PhpStorm 2016.3\jre\lib\ext: [access-bridge-32.jar, access-bridge.jar, cldrdata.jar, dnsns.jar, jaccess.jar, jfxrt.jar, localedata.jar, meta-index, nashorn.jar, sunec.jar, sunjce_provider.jar, sunmscapi.jar, sunpkcs11.jar, zipfs.jar] 
2017-03-28 13:54:44,755 [ 391] INFO - #com.intellij.idea.Main - JNU charset: Cp1252 
2017-03-28 13:54:44,927 [ 563] INFO - #com.intellij.idea.Main - JNA library (32-bit) loaded in 172 ms 
2017-03-28 13:54:44,974 [ 610] INFO - penapi.util.io.win32.IdeaWin32 - Native filesystem for Windows is operational 
2017-03-28 13:54:45,021 [ 657] INFO - #com.intellij.idea.Main - Using "FocusKiller" library to prevent focus stealing. 
2017-03-28 13:54:56,286 [ 11922] INFO - llij.ide.plugins.PluginManager - Cannot find optional descriptor plugin-intelliLang.xml 
2017-03-28 13:54:57,333 [ 12969] INFO - llij.ide.plugins.PluginManager - Cannot find optional descriptor js-nashorn-support.xml 
2017-03-28 13:54:57,474 [ 13110] INFO - llij.ide.plugins.PluginManager - Cannot find optional descriptor plugin-intelliLang.xml 
2017-03-28 13:54:57,958 [ 13594] INFO - llij.ide.plugins.PluginManager - Cannot find optional descriptor uml-java-support.xml 
2017-03-28 13:54:57,958 [ 13594] INFO - llij.ide.plugins.PluginManager - Cannot find optional descriptor uml-properties-support.xml 
2017-03-28 13:54:58,490 [ 14126] INFO - llij.ide.plugins.PluginManager - Plugin 'Markdown Navigator' can't be loaded because: Plugin is disabled 
2017-03-28 13:54:58,896 [ 14532] INFO - llij.ide.plugins.PluginManager - 67 plugins initialized in 3360 ms 
2017-03-28 13:54:58,927 [ 14563] INFO - llij.ide.plugins.PluginManager - Loaded bundled plugins: ASP (0.1), AngularJS (171.3780.104), Apache config (.htaccess) support (171.3780.104), Behat Support (171.3780.104), Blade Support (171.3780.104), CSS Support (171.3780.104), CVS Integration (11), Codeception Framework (171.3780.104), CoffeeScript (2.0), Command Line Tool Support (171.3780.104), Copyright (8.1), Database Tools and SQL (1.0), Docker integration (2.5.2), Drupal Support (171.3780.104), File Watchers (171.3780.104), GNU GetText files support (*.po) (171.3780.104), Gherkin (999.999), Git Integration (8.1), GitHub (171.3780.104), Google App Engine Support for PHP (171.3780.104), HTML Tools (2.0), Haml (171.3780.104), IDEA CORE (171.3780.104), Ini4Idea (171.3780.104), IntelliLang (8.0), JavaScript Debugger (1.0), JavaScript Intention Power Pack (0.9.4), JavaScript Support (1.0), Joomla! Support (171.3780.104), Less support (171.3780.104), Markdown support (VERSION), NodeJS (171.3780.104), PHP (999.999), PHP Docker (171.3780.104), PHP Remote Interpreter (171.3780.104), PHPSpec BDD Framework (171.3780.104), Perforce Integration (2.0), Performance Testing (171.3780.104), Phing Support (171.3780.104), QuirksMode (171.3780.104), REST Client (171.3780.104), ReStructuredText Support (171.3780.104), Refactor-X (2.01), Remote Hosts Access (0.1), SSH Remote Run (0.1), Sass support (171.3780.104), Settings Repository (171.3780.104), Subversion Integration (1.1), Task Management (1.0), Terminal (0.1), TextMate bundles support (VERSION), Time Tracking (1.0), Twig Support (171.3780.104), UML Support (1.0), Vagrant (171.3780.104), W3C Validators (2.0), WordPress Support (171.3780.104), XPathView + XSLT Support (4), XSLT-Debugger (1.4), YAML (171.3780.104), hg4idea (10.0), tslint (171.3780.104) 
2017-03-28 13:54:58,927 [ 14563] INFO - llij.ide.plugins.PluginManager - Loaded custom plugins: .ignore (1.7.6), Bootstrap 3 (2.4), CMD Support (1.0.5), Laravel Plugin (0.13.2) 
2017-03-28 13:54:58,927 [ 14563] INFO - llij.ide.plugins.PluginManager - Disabled plugins: Markdown Navigator (2.1.1) 
2017-03-28 13:55:04,396 [ 20032] INFO - ellij.util.io.PagedFileStorage - lower=100; upper=200; buffer=10; max=479 
2017-03-28 13:55:04,865 [ 20501] INFO - pl.local.NativeFileWatcherImpl - Starting file watcher: C:\Program Files (x86)\JetBrains\PhpStorm 2016.3\bin\fsnotifier.exe 
2017-03-28 13:55:05,036 [ 20672] INFO - pl.local.NativeFileWatcherImpl - Native file watcher is operational. 
2017-03-28 13:55:05,724 [ 21360] INFO - pi.util.registry.RegistryState - Registry values changed by user: 
2017-03-28 13:55:05,724 [ 21360] INFO - pi.util.registry.RegistryState - dumb.aware.run.configurations = true 
2017-03-28 13:55:05,724 [ 21360] INFO - pi.util.registry.RegistryState - search.everywhere.settings = true 
2017-03-28 13:55:12,123 [ 27759] INFO - rains.ide.BuiltInServerManager - built-in server started, port 63342 
2017-03-28 13:55:12,513 [ 28149] INFO - gs.impl.UpdateCheckerComponent - channel: release 
2017-03-28 13:55:14,073 [ 29709] INFO - il.indexing.FileBasedIndexImpl - Index exts enumerated:803 
2017-03-28 13:55:14,103 [ 29739] INFO - il.indexing.FileBasedIndexImpl - Index scheduled:25 
2017-03-28 13:55:14,551 [ 30187] INFO - tellij.psi.stubs.StubIndexImpl - All stub exts enumerated:348 
2017-03-28 13:55:14,567 [ 30203] INFO - tellij.psi.stubs.StubIndexImpl - stub exts update scheduled:26 
2017-03-28 13:55:15,616 [ 31252] INFO - j.ide.script.IdeStartupScripts - 0 startup script(s) found 
2017-03-28 13:55:17,465 [ 33101] INFO - plication.impl.ApplicationImpl - 81 application components initialized in 21929ms 
2017-03-28 13:55:17,481 [ 33117] INFO - .intellij.idea.IdeaApplication - App initialization took 38511 ms 
2017-03-28 13:55:17,825 [ 33461] ERROR - plication.impl.ApplicationImpl - null 
java.util.ConcurrentModificationException
 at java.util.LinkedHashMap$LinkedHashIterator.nextNode(LinkedHashMap.java:719)
 at java.util.LinkedHashMap$LinkedKeyIterator.next(LinkedHashMap.java:742)
 at com.intellij.util.containers.SequenceIterator.next(SequenceIterator.java:53)
 at com.intellij.ide.RecentProjectsManagerBase.b(RecentProjectsManagerBase.java:361)
 at com.intellij.openapi.application.impl.ApplicationImpl$2.run(ApplicationImpl.java:334)
 at java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:511)
 at java.util.concurrent.FutureTask.run(FutureTask.java:266)
 at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142)
 at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:617)
 at java.lang.Thread.run(Thread.java:745)
2017-03-28 13:55:17,856 [ 33492] ERROR - plication.impl.ApplicationImpl - PhpStorm 2017.1 Build #PS-171.3780.104 
2017-03-28 13:55:17,856 [ 33492] ERROR - plication.impl.ApplicationImpl - JDK: 1.8.0_112-release 
2017-03-28 13:55:17,856 [ 33492] ERROR - plication.impl.ApplicationImpl - VM: OpenJDK Server VM 
2017-03-28 13:55:17,856 [ 33492] ERROR - plication.impl.ApplicationImpl - Vendor: JetBrains s.r.o 
2017-03-28 13:55:17,856 [ 33492] ERROR - plication.impl.ApplicationImpl - OS: Windows 10 
2017-03-28 13:55:17,856 [ 33492] ERROR - plication.impl.ApplicationImpl - Last Action: 
2017-03-28 13:55:28,509 [ 44145] INFO - pl$FileIndexDataInitialization - Initialization done:14405 
2017-03-28 13:55:35,295 [ 50931] INFO - exImpl$StubIndexInitialization - Initialization done:6788 
2017-03-28 13:55:42,418 [ 58054] INFO - ellij.project.impl.ProjectImpl - 122 project components initialized in 15258 ms 
2017-03-28 13:55:42,793 [ 58429] INFO - le.impl.ModuleManagerComponent - 1 module(s) loaded in 375 ms 
2017-03-28 13:55:44,092 [ 59728] WARN - om.intellij.util.ProfilingUtil - Profiling agent is not enabled. Add -agentlib:yjpagent to idea.vmoptions if necessary to profile IDEA. 
2017-03-28 13:55:44,420 [ 60056] INFO - .openapi.application.Preloader - Finished preloading com.intellij.openapi.actionSystem.impl.ActionPreloader@1c60b8f 
2017-03-28 13:55:44,623 [ 60259] INFO - PerformancePlugin - Performance Plugin is in silent mode 
2017-03-28 13:55:46,139 [ 61775] INFO - .openapi.application.Preloader - Finished preloading com.intellij.ide.ui.search.SearchableOptionPreloader@229453 
2017-03-28 13:55:47,280 [ 62916] INFO - .openapi.application.Preloader - Finished preloading com.intellij.codeInsight.completion.CompletionPreloader@390fc1 
2017-03-28 13:55:48,233 [ 63869] INFO - ellij.project.impl.ProjectImpl - 23 project components initialized in 125 ms 
2017-03-28 13:55:53,528 [ 69164] INFO - tartup.impl.StartupManagerImpl - OpenFilesActivity run in 4334 
2017-03-28 13:55:54,044 [ 69680] INFO - .diagnostic.PerformanceWatcher - Pushing properties took 4631ms; general responsiveness: ok; EDT responsiveness: 1/4 sluggish, 3/4 very slow 
2017-03-28 13:55:54,122 [ 69758] INFO - tartup.impl.StartupManagerImpl - InitToolWindowsActivity run in 594 
2017-03-28 13:55:54,719 [ 70355] INFO - tartup.impl.StartupManagerImpl - JsbtStartupActivity run in 545 
2017-03-28 13:55:56,123 [ 71759] INFO - tartup.impl.StartupManagerImpl - D:/GitHub/RS&H/watts/.idea case-sensitivity: expected=false actual=false 
2017-03-28 13:55:56,682 [ 72318] INFO - .diagnostic.PerformanceWatcher - Indexable file iteration took 2607ms; general responsiveness: 1/3 sluggish; EDT responsiveness: 0/3 sluggish, 1/3 very slow 
2017-03-28 13:55:56,682 [ 72318] INFO - indexing.UnindexedFilesUpdater - Unindexed files update started: 851 files to update 
2017-03-28 13:55:57,319 [ 72955] INFO - tor.impl.FileEditorManagerImpl - Project opening took 30660 ms 
2017-03-28 13:56:29,718 [ 105354] INFO - j.ide.startup.FileContentQueue - The system cannot find the file specified 
java.io.IOException: The system cannot find the file specified
 at java.io.FileInputStream.readBytes(Native Method)
 at java.io.FileInputStream.read(FileInputStream.java:255)
 at java.io.BufferedInputStream.read1(BufferedInputStream.java:284)
 at java.io.BufferedInputStream.read(BufferedInputStream.java:345)
 at com.intellij.openapi.vfs.impl.local.LocalFileSystemBase.a(LocalFileSystemBase.java:466)
 at com.intellij.openapi.vfs.impl.local.LocalFileSystemBase.contentsToByteArray(LocalFileSystemBase.java:457)
 at com.intellij.openapi.vfs.newvfs.persistent.PersistentFSImpl.contentsToByteArray(PersistentFSImpl.java:502)
 at com.intellij.openapi.vfs.newvfs.impl.VirtualFileImpl.contentsToByteArray(VirtualFileImpl.java:127)
 at com.intellij.ide.caches.FileContent.getBytes(FileContent.java:51)
 at com.intellij.openapi.project.FileContentQueue.a(FileContentQueue.java:139)
 at com.intellij.openapi.project.FileContentQueue.a(FileContentQueue.java:115)
 at com.intellij.openapi.project.FileContentQueue.a(FileContentQueue.java:99)
 at com.intellij.openapi.project.FileContentQueue.b(FileContentQueue.java:84)
 at java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:511)
 at java.util.concurrent.FutureTask.run(FutureTask.java:266)
 at com.intellij.util.concurrency.BoundedTaskExecutor$2.run(BoundedTaskExecutor.java:212)
 at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142)
 at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:617)
 at java.lang.Thread.run(Thread.java:745)
2017-03-28 13:56:29,719 [ 105355] INFO - j.ide.startup.FileContentQueue - The system cannot find the file specified 
java.io.IOException: The system cannot find the file specified
 at java.io.FileInputStream.readBytes(Native Method)
 at java.io.FileInputStream.read(FileInputStream.java:255)
 at com.intellij.openapi.vfs.impl.local.LocalFileSystemBase.a(LocalFileSystemBase.java:466)
 at com.intellij.openapi.vfs.impl.local.LocalFileSystemBase.contentsToByteArray(LocalFileSystemBase.java:457)
 at com.intellij.openapi.vfs.newvfs.persistent.PersistentFSImpl.contentsToByteArray(PersistentFSImpl.java:502)
 at com.intellij.openapi.vfs.newvfs.impl.VirtualFileImpl.contentsToByteArray(VirtualFileImpl.java:127)
 at com.intellij.ide.caches.FileContent.getBytes(FileContent.java:51)
 at com.intellij.openapi.project.FileContentQueue.a(FileContentQueue.java:139)
 at com.intellij.openapi.project.FileContentQueue.a(FileContentQueue.java:115)
 at com.intellij.openapi.project.FileContentQueue.a(FileContentQueue.java:99)
 at com.intellij.openapi.project.FileContentQueue.b(FileContentQueue.java:84)
 at java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:511)
 at java.util.concurrent.FutureTask.run(FutureTask.java:266)
 at com.intellij.util.concurrency.BoundedTaskExecutor$2.run(BoundedTaskExecutor.java:212)
 at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142)
 at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:617)
 at java.lang.Thread.run(Thread.java:745)