If I understand what is being said, that all quests completed are not registered as completed, that is something that cannot be reversed on an account/character as that is saved server side.

Try restarting the game. Heck, restart the PC while doing that to be safe. They log back in.

If that does not work, @ZOS_Kevin or @ZOS_Bill may be able to help though this is a holiday so you may have to wait until tomorrow.

If you haven't played for 3 years your friends may have unfriended you.

I assume that if they logged in on the "wrong" server, it would be pretty obvious by the lack of any characters-- unless they had previously created identical (or very similar) characters on both servers.

One possibility is that the account had been moved to cold storage, which means it would have taken longer to log in due to the account needing to be retrieved from cold storage. A few years ago I had an issue with crafting stations where they were not showing my researched traits, presumably because the data wasn't being loaded before I checked the stations to see my progress, but everything reappeared later. That was before cold storage was implemented, but maybe this is something like that-- the necessary data isn't accessible yet for whatever reason? The suggestion to log out, shut down the game, reboot the computer, and try again might help.