I got a letter from the IRS saying I need to send in my cancelled rent checks?
The wording of your post indicates to me that you are not a landlord, but instead are a paying renter, and that you applied for rental assistance.
First, I doubt the letter was from the IRS. If anything, it was probably from your state taxing authority.
Second, you need to provide proof that you actually paid rent with the assistance funds provided. It may not necessarily be in the form of a cancelled check. I can't state for sure, but I would think receipts from the landlord acknowledging they received your rent payments would suffice. Without more details to work with, that's all the information I can offer. Weather it's helpful or not is unknown.
