If I overlap two clips with Auto Crossfade on, the clips get a fade-in/fade-out respectively, replacing any fades I might have had previously.
 
If I change my mind and pull them apart again, the auto fade-in/fade-outs stay on the clips. I have to return the clips to their original state manually.
 
 
Reaper restores the clips to their original condition when you pull them apart.
Reaper even remembers previous manually applied fades and restores them.