Redirect to main site’s sign-up for a renamed subdomain

I had a subsite with abc.example.com, and recently I changed it to example.com by renaming in multisite’s network admin. Since then, whenever I try to visit that subdomain by clicking WP’s internal links (like dashboard, visit….), I end up with mainsite’s sign-up page.

I figured that it is because the renamed subsite is not ‘registered’ in the multisite network system.

So I tried to change it in my DB manually, and I also used ‘Search and Replace’ plugin. I thought I pretty much changed all values manually, but it still doesn’t work. By ‘Search and Replace’ plugin, it gives critical error when I do a dry run.

I guess I just have to change the domain’s name value in a few more entries in DB, but can’t figure out where.

Any advice?