Normally when restoring from backup, you’d also restore a snapshot of your database from backup. Is that what you did? The file meta data is actually stored in the database.
Are the restored files in the same underlying storage path they were in before or did you restore into a different spot or change anything else during the course of restoring things?
Also, to clarify, what was the original issue? What were you doing involving git?
P.S. It would also be helpful if you posted your real parsed config (using occ config:list system) and app lists (using occ app:list) as noted in the support template).