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Presumably, your brother is also on the deed & the mortgage also. As such he is fully liable for the mortgage as is his partner. (As an aside, if this is going to be the same situation in the future your brother should have his social security number listed on the mortgage).
You can try to do what you suggest but the IRS may ask for further evidence such as copies of the checks with your brother's signature on them, if he pays by check, although that shouldn't be necessary; you might consider sending a copy of one cancelled check (copy both sides) & state that the remainder are available upon request.
In any event, it should eventually be straightened out; it just takes time. By the way, did the IRS ask for anything else specifically? If they did, you'll want to comply with the request in order to avoid additional correspondence.
Did you prepare their return, or what role are you playing in this process? The reason that I ask is that you'll want to make sure your brother signs any correspondence with the IRS.
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