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.
In my case, this was caused by using the same Git repo from both admin and non-admin command prompts. When last git pull was from admin cmd, the index was created by it, and then non-admin cmd had insufficient permissions to modify it.
My solution was re-creating the index (while keeping the worktree intact):
del .git\index
git reset --mixed head