I have solved my problem, after about a day's worth of troubleshooting.
Enpass 6.x does not handle spaces correctly in the webdav url. Spaces in a url should be encoded as %20, and that's what I tried. It would always fail to sync.
If I put them into a path that had no space, I could get it to sync to any arbitrary folder, so it wasn't a problem with arbitrary paths.
When I however use an actual space character in the url (instead of url encoding) suddenly it started working. I will now begin the process of upgrading to 6.x on all my devices (5.x was getting rather painful at this point, since there haven't been browser plugins in a long time). Mostly I was forced to figure it out, since iOS decided to upgrade my phone without my permission.