This issue has been outstanding for some time. There's no official solution to this which makes little sense considering the time this has been an issue and the destructive nature of doing a push after moving a file.

Here's the procedure we use when moving files:

1. Before moving files, always do a push/pull and make sure that there are no outstanding changes.
2. Move the files.
3. Reset the changes from step 2: sf project reset tracking

This is very manual and if you forget step 1 before step 2, your next push deletes files and makes a