So Unity 2018.3 and the new prefab workflow came out! Wow! There are great new features in there. In fact, for all of you who are using my own nested prefab solution called prefab helper: stop! Really, I mean it. The prefab helper is a crutch, now that the official full featured solution is out there, go with the new prefab workflow. Anyway, I' not really give you guys a choice, I'm deprecating the prefab helper in version 1.3.1 and in the next Dungeon Master major release, I will eliminate the prefab helper completely.
Okay, now for the bad news. The Dungeon Master used the previous prefab system extensively: to create rooms, levels, keep references, etc. A lot of these things broke down with the new prefab workflow. I got a couple of bug reports with various issues I need to address. I already released a hotfix (v1.3.1a) and I'm in the process of fixing other things, so another hotfix (1.3.1b) should be available soon. To all of you who are having issues with the Dungeon Master: don't worry, I'm on it! That being said, if you have good recipes to reproduce bugs, please send them to me, I might not know all of them yet.
Hopefully, all of this will be solved soon. Thanks for your patience!