Using the GitHub Windows client I did a sync to pull remote changes to my local machine, but before finishing the sync, I ran out of disk space and the sync failed.
For me it was this error:
Rename from 'D:/dev/repo/.git/refs/remotes/origin/my-branch.lock' to 'D:/dev/repo/.git/refs/remotes/origin/my-branch' failed. Should I try again? (y/n)
Renamed "my-branch" file, retried, and "my-branch.lock" succeed in renaming, not sure if this is correct, but worked. Local changes in both master and my-branch were preserved.