So I have been having this same problem, and may have stumbled across a solution…
So I was just tinkering, seeing what happened if I did different things. So I deactivated all plugins site-wide, reverted back to default theme, and it was still happening. It WASN’T happening on the default permalinks, so I thought I was on the right track.
So I jumped in my FTP client, and saw that .htaccess was actually written as .htaccess.txt. No idea why, but I knew it had to be .htaccess. So I renamed it, and so far, the website is back to normal, with the custom theme activated, plugins going, and the standard %postname% permalinks activated.
Hope this helps some of you guys
