I would guess that, if it's ever happened, it would be highly unlikely. I'd wager the odds go down drastically the higher ranked the school.
I say that based on my observations (from the board and my own applications) regarding the transfer process. It seems like most schools admit their first round draft picks, so to speak, reject a good deal either right away or a bit later and keep a few to several on standby.
I'd bet the size of the standby group varies by school -- at a higher ranked/more national school, they probably need less people on standby, because they presume that the majority of those offered admission will attend. I'd say this especially applies to Yale, Harvard, Stanford, Columbia, NYU and Chicago, and to a lesser extent the rest of the T14 (depending largely on school and number of transfers they admit). In any event, it seems like most schools keep some on standby -- the chances of the school exhausting that list and then going back to the applications they rejected is slim to none.
For instance, Harvard just admitted their first picks. They also rejected a great deal of people. Evidently, from the boards, a few people are still in limbo. I'd guess those limbo people might be their standby group, for those transfers that choose another school (Yale, Stanford, or another top school based on $ or location).
Anyone else have thoughts on this? It bears mentioning that I could be completely wrong -- this is all based on personal observations. Personally, I don't think you have anything to lose by calling, but who knows.