Git version 2.8.0 (sorry can't update to more recent on my machine) on Ubuntu. After moving a file, if the new file is in the index but the deletion of the old file is not staged, git stash loses the deletion operation. Repro: 1. git mv a b This will have both the "deletion" and the "file added" in the index 2. git stash; git stash pop Now file a is still in the index, but file b deletion is not staged. 3. git stash; git stash show -v This will show that the deletion operation is not in the stash 4. git stash pop Again confirms the issue, file a is in the index, but file b is present and unmodified in the working directory.