We have a situation where were are using git to stash myriad scans (images) and do not wish to preserve them on the local machine once set on up; however, git is seeing each loc
For each file to be deleted, do this:
git update-index --assume-unchanged
This should stop Git from asking you to commit the deletion.
That being said, perhaps a better solution would be to use SFTP with permissions set to disallow deleting or modifying files once uploaded.