Hello, Falcon Scholar here. I am in the same boat, my prep school said they would send out transcripts soon. My file was not closed however. Application still shows as incomplete, with "College Transcripts" missing. I had contacted academy admissions about this about a month ago, and they said not to worry.
This is the case at my FFS prep school, and I am sure it is the same at all the others. The director of academy admissions will be meeting with the prep school directors to make sure all the applications for Falcons are good to go. I'm sure if it was a real issue we would be contacted and given the opportunity to fix it.