Tile and Hardness Editing
This problem wasn't occurring until about...today. I was switching around tiles which had editor hardness (the kind you place manually, not default hardness like on the cliffs), and realized that the hardness was being replaced with the tile's hardness, so it was just disappearing. Example: If I change the tiles under a house from grass to pavement, the house's hardness disappears. I'm not sure what's causing this, as hardness and tiles had been separate until I started editing stuff today, and I can't think of anything I've done that could have messed with hardness/tiles. The problem persists across all D-Mods and editors (WDE, WDE+, and all versions of WDE+2).
It's always been there, as far as I know. You probably just noticed it now. You might want to check out some old screens you think this might have also happened on. It happened to me once and I had to go and edit back roughly over 10 screens.
This always happened to me in every DMOD I've ever tried making. It's a horrid glitch that has never been fixed and is one of the main reasons I don't make DMODs. >_>
You could use just DinkEdit. (Possibly the FreeDink version, if the original doesn't run on your computer.) Of course there's no need to do everything in DinkEdit, you can still keep using WDE for most things and only load up DE when you need to perform that specific task.