Zone Doctor+ problem

Yeah, just this week I realized that ignoring the error message at saving does not cause later problems... so far I haven't tried editing the tilesets themselves, only the map tiles like normal.

Your comment is very timely though, I'd like to ask you about the possibility of using different combinations of tilesets in one same map. I might be mistaken but it looks like Zone Doctor gives you the option to switch a map's default layers (1, 2, 3) to the layers of a different tileset; like, say, opening the Zozo town map and switching its default "layer 2" to the layer 2 of Castle Figaro or something. Making odd combinations like that. I don't know if it's viable but it could lead to some interesting scenarios.

I quite like messing with map editing, I think I have a good eye for it.

About importing maps -- that's bad news for me, I have the habit of exporting/importing my edits, for backup purposes. Do you just backup the entire rom, then?

Changing the default tileset for a map should be fine although it would require some trial and error as I have not done it much myself.  The game itself does this already though.  You can see a few maps that use multiple tilesets depending, one example is Figaro basement and the Opera House beind on the same map file, but each area uses a different tileset so you can see where the tilesets of part of the map are garbage depending on what you are looking at.

The program itself has an option for auto backup that you can use, I just personally prefer to do manual full ROM backup before any big changes.  It makes it alot easier to see what you did wrong if you are having crashes.

The main things that cause crashes or that make the editor mess up is event editing or importing maps.

You may see some overworld map corruption if you do manual hex editing within ZD but there is an easy fix for this.

EDIT: Also keep in mind that there are alot of shared maps so if you make an edit on one this will carry over to other maps.