Yeah, it still stays there, but in Y, you get no credit to your SQ account. I've noticed it many times, and the only reason I can come up with for them wanting it there are:
(a) It simplifies their computer system to have the accounts connected all the time, and only credit when in J or P
(b) Just in case you decide to spend thousands of dollars and upgrade ot J or P, you won't miss out on your rightfully entitled PPS credit

Anyway though, it isn't anything to worry about.