One of my reclaim hosted WordPress mulisites recently was returning 404 on all links to any of the sub sites (st up directory based).
Following a hunch I noticed the the site’s htaceess file had ben wiped out of the code multisite generates and only include what looks like cpanel generated htaccess for PHP issues-- this was the entirery of my WordPress site htaccess:
I hope this was a one time error, as I imagine for many users thy would not know where to check. If cpanel is adding to an htacess file should it not first save a back up of the file it is replacing?
Posted here more as a reference in case others find this happening.