How to fix Cannot create a new backup. A previous backup already exists in refs/original/ in Git

The simplest solution is to add the -f (force) flag to your filter-branch command. This tells Git to remove the existing backup and create a new one:

git filter-branch -f --tree-filter 'your-filter-here' HEAD

Or for other filter types:

git filter-branch -f --env-filter 'your-filter-here' -- --all

Warning: Using -f will delete your existing backup refs. Make sure you don't need them before proceeding.

If you want to explicitly remove the backup refs before running filter-branch again, use this command:

git for-each-ref --format='delete %(refname)' refs/original | git update-ref --stdin

This safely removes all refs under refs/original/ using Git's own reference management. Alternatively, you can delete them one by one:

git for-each-ref --format="%(refname)" refs/original/ | xargs -n 1 git update-ref -d

After removing the refs, run your filter-branch command normally.

If the git commands don't work (for example, if refs are corrupted), you can delete the backup directory directly:

rm -rf .git/refs/original

Important: If you've run git gc, the refs might be packed. Check and edit .git/packed-refs to remove any lines starting with refs/original/:

# View packed refs containing 'original'
grep refs/original .git/packed-refs

# If found, edit the file and remove those lines
# Then run garbage collection
git gc --prune=now

After your filter-branch operation succeeds and you've verified the results, perform a complete cleanup to reclaim disk space:

# Remove backup refs
git for-each-ref --format='delete %(refname)' refs/original | git update-ref --stdin

# Expire all reflogs immediately
git reflog expire --expire=now --all

# Run aggressive garbage collection
git gc --aggressive --prune=now

This removes all traces of the old history and can significantly reduce repository size, especially if you removed large files.

Confirm that all backup refs have been removed:

# Should return nothing
git for-each-ref refs/original/

# Check the directory doesn't exist
ls .git/refs/original/

# Verify packed-refs has no original entries
grep refs/original .git/packed-refs

If all commands return empty or "not found," you can safely run filter-branch again.