If you are using Git Gui on windows,
- Abort the merge
- Make sure you are on your target branch
- Delete the conflicting file from explorer
- Rescan for changes in Git Gui (F5)
- Notice that conflicting file is deleted
- Select Stage Changed Files To Commit (Ctrl-I) from Commit menu
- Enter a commit comment like "deleted conflicting file"
- Commit (ctrl-enter)
- Now if you restart the merge it will (hopefully) work.