I had problems with the update on a previous pihole install already up and running with unbound and cloudflared. Did the v6 update as soon as it dropped just for some excitement. During install I did not disable lighttdp or remove it. When I started having failures to access the web portal it had to do with lighttpd running, stopping and disabling it with systemctl fixed most of my problems.

https://discourse.pi-hole.net/t/cannot-access-web-interface-after-pihole-6-update/77366/4

The git fsck failing showed a corrupt repository so I researched how to repair a git repository and found the tool git-repair - installed and ran this with the --force flag and this repaired the repository.

Then ran git pull and the repository was now healthy. My web UI also works now!!

Probably a silly feature request but would it be worthwhile to add a git fsck to all the pihole stores in the debug script?

To start you should go to your web admin folder at /var/www/html/admin and run a git fsck to make sure you’re having the same problem as the person above. If you get a lot of failures, its likely the same issue.

So based on this resolved thread, it looks like you need to install git-repair and then once again go to your pihole web admin interface folder at /var/www/html/admin.

Then once in that folder run git-repair --force and then when that completes run git pull. Hopefully that resolves this issue for you.