You know how it's hard to make the map editor erase things like gold and stone mines? At least with them you can change to terrain and put some water there to destroy the gold if you placed it in the wrong spot.
This still will not destroy rocks. I discovered that the answer is to use map copy and copy a small amount of desert or water or whatever you want where the rocks (or mines) are and put the copied object where the rock is.
That's how to erase rocks if you stick them in the wrong spot. It's out-of-the-way, but more effective than re-loading your scenario.
I'm going back to find out if it works on flags as well. If you must post a, "duh", then go ahead, but could you please post an answer to that question so I won't have to post another one of these newbie things. Please? It would save space.