CLion not showing actual file contents

I am just about to pull the trigger and buy my first year of CLion subscription, given the excellent features, but one thing happened last night that has caused me to pause.

While removing some code from a .cpp file, CLion gave the error "unable to open the file for writing", however the file in the editor looked like it had been edited and the on-disk version had not.  This of course, caused compile errors.  I tried closing CLion but when it restarted it still showed me it's incorrect version of the file and not the real on-disk version, and the only way I could solve this was to edit the file using VSCode.

So there are two issues here - firstly that CLion had issues writing changes to disk and secondly it had its own version of the file somewhere (cached or something?).  I am wondering if this would be caused by having Git Kraken open on the same source tree, and that's also checking for file changes.