You musn't save the map after you pressed "Change Tileset" or something, otherwise it will save it over the file that you changed the tiles from.
So Simply:
1. Create Map and Save it.
2. Press Edit Tileset and select the tiles you want.
3. Press "Okay" or what ever it is on the Tileset chaging thing.
4. Do not save the map, instead just press the Red X and restart the editor.
For me this works, if I save the map after step 3 the tiles won't change.
And, you can edit the map further with Normal editor and it should work fine (as far as I know (correct me if I am wrong)) you can save it and stuff, just remember that if you exceed limits like in Doodads or Units or such things you must remove all the doodads and units taht are over the limit (which is kinda impossible without loosing the progress)) and also you can not have them both opened so, check first if you can still save the map.