It will be on hold until the updated transcripts are received by aacomas. If you know that you'll get secondaries at the schools you'll apply to, finish the secondaries and send a message to the admissions dean/counselor and ask if they are willing to place a hold on your file until aacomas sends an updated application w/ the new gpa's. That is currently my situation as I just finished 3 re-takes and will be sending updates transcripts in a couple of days. The schools I contacted said they would be happy to hold my file until then.