Pship client (and 1040 partners) were audited. Mid audit the taxpayer presented to the auditor R&D credits (third party consultant did the study)for consideration. After a few weeks she responded the service did not have time/personnel to review and to address the credits after the audit. 2 years later the adjustments by the auditor were agreed to. 4549 issued 4/2020.
I asked a Tax attorney friend during the audit his opinion. He said to file and amended return after the audit because the credits were not part of the audit nor were they on the original return. He said appeals will kick it because there is nothing to appeal. He has experienced it before.
In response to your question is there time remaining on the statute of limitations for the partnership? If so, file a 1040X for the partnership to claim the credits if they were incurred within the proper calendar year, I assume from your message the audited year.