PHPStorm Changes in memory differs from filesystem

If I change a lot of files (100+) via search and replace, file/folder compare etc., PHPStorm does not actually change them all. For example:

I compare folder A with folder B and apply changes. Now I have to "Reload all from Disk" to check, if the changes were made. If I forget this and restart PHPStorm, around 20 files were not changed. I also don't get the popup with the "memoy differs from file..." hint every time. All files are locally. I upload them first after

This is getting a real pain, because I have to compare, reload from drisk and compare again. Yesterday I had to do this five times (!!!). The worst part? Today I made a change to a file (lets name it foo.php) I compared and edited yesterday, the popup with the hint "locally file differs from remote" appeared as PHPStorm wanted to upload it. I compared them and the remote file was still the old before I compared (yesterday) both folders A and B. I again compared A and B an et voila, foo.php still differs.

I don't have to tell you, what problems this causes for me, because I always have to check, if PHPStorm made the changes. No problems with remote or git files though. Only local.

OS: Win10
PHPStorm: newest