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All of my transcripts were processed two days ago and I've been waiting for my Academic Summary Report to come out. I applied for a fee waiver but am still waiting for the non-filer tax documents to get mailed to me from the IRS so I can send them to LSAC. This afternoon I realized that I could use the conditional fee waiver to purchase the CAS.
I purchased CAS but I have an alert (It's been there for several weeks actually) that says there is a hold on my account regarding my fee waiver. Will I still get my Academic Summary Report before I send my tax documents to LSAC? I don't get why they can't just upload it seeing as I now purchased CAS using the conditional waiver.

Call them bro.

I think your problem is too specific for us to answer. Your best bet is to call to know for sure.

I don't get why they can't just upload it seeing as I now purchased CAS using the conditional waiver.

Remember that LSAC and law schools have thousands of applicants during this time, so please be patient. Its only been 2 days.