I am working in WebStorm, not sure if it's WebStorm or Git issue.
I have only changed 3 files, the changes normally show only them. Once I leave the IDE, then come back and I see the whole project (1127 files) as deleted in the changes.
When I try to reset to head it rolls everything back to 3 files, waiting 5 min and all the 'deleted' files are there again. It is an infinite loop of despair.
I've tried resetting to head, it helps for 5 min and all over again.
If you're on Mac it might be because you keep your project in the place where it syncs it with the cloud.
Try cloning the project into a place like ~/dev/project_name