Following
this post that describes the problem, some more info:
This is more or less what happens in the background when the issue occurs (apart from the more obvious resetting columns in that account):
The option in question (issue occurs when that is enabled in a custom folder - or Label, as Google calls them).
If the option is disabled, the only way to sync/download messages for that folder is to simply click on it (in Epyrus), and this works normally.
Epyrus 2.0.1, Win 10