FileNotFoundException after upgrading my plugin from 2016.1.3 to 2017.1.3

After upgrading my plugin from 2016.1.3 to 2017.1.3 I get the following exception when building a project with my custom compiler (jps-plugin). I tried on two different development environments (Windows and Ubuntu) with the same result.

The system path looks incorrect in the error, I didn't change it from the default, in fact I see the following option the "Console" when debugging my plugin (running IntelliJ with my plugin from code): "-Didea.system.path=C:\Users\Kobus de Bruyn\.IdeaIC2017.1\system\plugins-sandbox\system" 

Any idea on what the issue might be will be appreciated.

Error:Internal error: (java.lang.RuntimeException) java.io.FileNotFoundException: C:\Program Files\JetBrains\IntelliJ IDEA Community Edition 2017.1.2\system\index\indices.enum (The system cannot find the path specified)
java.lang.RuntimeException: java.io.FileNotFoundException: C:\Program Files\JetBrains\IntelliJ IDEA Community Edition 2017.1.2\system\index\indices.enum (The system cannot find the path specified)
 at com.intellij.util.indexing.ID.writeEnumFile(ID.java:139)
 at com.intellij.util.indexing.ID.<clinit>(ID.java:75)
 at org.jetbrains.jps.backwardRefs.index.CompilerIndices.<clinit>(CompilerIndices.java:43)
 at org.jetbrains.jps.backwardRefs.CompilerBackwardReferenceIndex.<init>(CompilerBackwardReferenceIndex.java:85)
 at org.jetbrains.jps.backwardRefs.BackwardReferenceIndexWriter.initialize(BackwardReferenceIndexWriter.java:98)
 at org.jetbrains.jps.backwardRefs.BackwardReferenceIndexBuilder.buildStarted(BackwardReferenceIndexBuilder.java:53)
 at org.jetbrains.jps.incremental.IncProjectBuilder.runBuild(IncProjectBuilder.java:372)
 at org.jetbrains.jps.incremental.IncProjectBuilder.build(IncProjectBuilder.java:192)
 at org.jetbrains.jps.cmdline.BuildRunner.runBuild(BuildRunner.java:138)
 at org.jetbrains.jps.cmdline.BuildSession.runBuild(BuildSession.java:295)
 at org.jetbrains.jps.cmdline.BuildSession.run(BuildSession.java:125)
 at org.jetbrains.jps.cmdline.BuildMain$MyMessageHandler.lambda$channelRead0$0(BuildMain.java:236)
 at org.jetbrains.jps.service.impl.SharedThreadPoolImpl.lambda$executeOnPooledThread$0(SharedThreadPoolImpl.java:42)
 at java.util.concurrent.Executors$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:748)
Caused by: java.io.FileNotFoundException: C:\Program Files\JetBrains\IntelliJ IDEA Community Edition 2017.1.2\system\index\indices.enum (The system cannot find the path specified)
 at java.io.FileOutputStream.open0(Native Method)
 at java.io.FileOutputStream.open(FileOutputStream.java:270)
 at java.io.FileOutputStream.<init>(FileOutputStream.java:213)
 at java.io.FileOutputStream.<init>(FileOutputStream.java:162)
 at java.io.FileWriter.<init>(FileWriter.java:90)
 at com.intellij.util.indexing.ID.writeEnumFile(ID.java:117)
 ... 17 more