There are two reasons for receiving emails regarding affiliate programs being deleted.
The first reason is if the program was actually deleted. You will need to find another merchant to promote (if the mearchant isn’t on another affiliate network – if so, just switch to that).
The second reason is if you’re using the API functionality. If affiliate programs are imported automatically, somethings glitches happen (from the affiliate network). Next time the API is updated, everything should be back to normal again.