Clearly, the income must be reported as partnership income on the partnerships's form 1065 return, even if the partnership is not issued a 1099 of any kind.
If this is for 2023 taxes, your son can request the 1099 in his name be cancelled and re-issued. If that fails, then your son has 3 options.
a. File by mail. Leave the income off the return. Attach a copy of the 1099 and a written explanation. (Don't send detailed proof, but keep records in case of followup.)
b. Ignore the income. (The IRS may send a bill for taxes for the missed income, he would reply with a letter of explanation and a copy of his proof.)
c. Add the income, then zero it out with a negative offsetting entry. (The IRS may send a request for clarification, he would reply with a letter of explanation and a copy of his proof.)
