This happens now for some time; I didn't update my Git and TortoiseGit for a long time, but I update Creator regularly.

I think starting with Creator 4.2, the following happens:

• Start an Interactive Rebase
• Move some files around so there are (trivial) merge conflicts
• In some cases, I get the message box to run merge tool, but I don't see the merge tool (may be related to "reload documents" message boxes that appeared before)
• Another message box pops up (I don't remember exactly now, will fill later when reproduces)
• Git status now shows that the file with conflicts is deleted
• You can now abort the rebase and start again, and there are good chances that the process finishes successfully

Two notes:

• The files that are modified by Interactive Rebase are open in editors which leads to "reload" message boxes
• The files are on a network drive, so the whole process takes some time

I try to create a video and append it here.