timthetryhard:
Is it safe to assume you are applying for Wharton R2? If so, I would email the admissions office directly and ask them the best way to handle this matter. You should get a timely response well in advance of the application deadline.
In the interim or as an alternative, you can combine the transcripts into one PDF (through Adobe or manual scanning) and upload them as a singular file. As long as they are clearly demarcated within the file (you can put a labeled page break in between them), the Admissions Committee should have no problem identifying which courses/grades are associated with which program and during which time. If the common belief is that admissions committees are reviewing candidates' background details with a fine-tooth comb, you can rest assure that they are recognizing this separation of transcripts with the same attention to detail.
Hope that helps,
Seth
https://admissionado.com/