If by "send out your applications to other programs" you mean add more schools on your designation list, I'm pretty sure you can always do that. I don't think you have to or should wait for the whole academic update thing. I believe if PTCAS receives the transcripts after the newly added schools receive your application from PTCAS, PTCAS will alert the schools on the updated transcript when it comes in or the schools will recheck PTCAS, I don't know exactly how it works but I don't believe you are in control of that so I'd just do whatever I could ASAP, add designations, update PTCAS with Fall grades, E-Submit etc.. I may be totally off on what you are exactly asking but that's what I think.