Looks like it's a result of Bug 1694942 - the mbox->maildir conversion doesn't realise that
filterlog.html is a special file (sigh) and just treats it as an mbox and converts it into a maildir.
Then later, when filters are run upon a folder in that converted account, it tries to write to the filter log. This fails and the filters are stopped dead.
(nsMsgFilterList::EnsureLogFile() is one culprit. I think there might be a couple of others, maybe one in junk filtering?)
First part of the fix is simple enough: modify the filter running procedure so it can keep going even without logging.
Secondly: Fix Bug 1694942 so that
filterlog.html is never converted into a maildir in the first place.
Thirdly: we need to deal with existing
filterlog.html directories out in the wild. A bunch of intrepid users have already switched to maildir and we should make the experience as smooth as we can for them. Easiest thing is to just delete such directories when we see them, either as part of a migration phase on startup, or on-the-fly.
I've started on these fixes (with a few false starts!). In the meantime, the easiest workaround is to check for
filterlog.html directories and manually delete them!