Not submitting separate transcripts for colleges all on one transcript

I am working on grad school applications, and I have a question about my transcript uploads. I took community college classes from several colleges in the same district in high school, and the district only provides one comprehensive transcript with classes from all colleges, which I just uploaded for the first college, and assumed it was unnecessary to upload for all the other ones. However, after I submitted, the portal for the application I am currently working on is showing that I am missing transcripts for the other schools, so I was wondering if it would still be processed. I did email the grad advisor, but it is due in a few days, so I'm unsure if they will get back to me before then. I am still able to upload documents for these schools, but I don't want to reupload the same document multiple times. Should I just put a note in place of a transcript upload saying that it is included on the one comprehensive transcript, or something else?

For most of the other applications, I was able to put the school name as the district, and just uploaded the one transcript, but there were at least a few applications that I had to put the individual colleges, in which I also only uploaded the one transcript for one school. My main concern is that I will get an automatic rejection for having an incomplete application, even though all my records are there. Will admissions committees review it anyway, or should I reach out to these schools that I have already submitted my applications?

Just submit the same transcript multiple times.

I would guess (guess) that it will be all right, but you can't trust or depend on such a guess.

I suggest that you start the process of obtaining the other transcripts and simultaneously, contact any university that has expressed concern to get actual guidance.

Most grad school applications are handled by humans (not, thankfully AI's) so the facts should become clear. But start the formal process so that all the i's are crossed and the t's dotted. ;-)