I couldn't find a solution to this either. Ultimately what I did was just reloaded the data files without setting an active file, duplicated the cell I was trying to mod, saving it as a new esp, and then just used that one. You'll need to manually replace any custom objects you have, though.
I found that this always happens to me if I go to a cell and right-click something in the render window, that seems to be a sure way to mark it as edited. So I just select it in the render window, and then right-click it in the cell's object list, and that works just fine 90% of the time. Otherwise, just save often in case something gets messed up I guess.