Hi guys, I've been following this thread (and threads similar to this one) for some time having experienced the same issues with un-editable terrain.
I just wanted to confirm what worked for me.
First thing I've done was to correct the game and editor paths in "Options\Preferences". What I actually had to do was to put capitalised "Data" and "Editor". This alone allowed me to save new levels correctly and edit them again after re-opening the engine.
To edit old modules what I did was what Baardvark said. I copied files from Data\Mods\"Modname"\Levels\"levelname" to Data\Editor\Mods\"Modname"\Levels\"Levelname".

Worked like I charm. Thank you guys for investigating this issue :)