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I can’t think of a reason why the IRS would ever ask to see canceled rent checks. Are you sure the request did not come from your state income tax department? If you received a state renters rebate or renters credit, the state might be interested in knowing how you paid your rent, because it might affect your qualifications for the rebate. I don’t think the IRS will ever care about your rent.
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.