I assume that you didn't have any problems filing returns with the wrong PTIN? In which case what is the point of having one?
Strange that you got a phone call instead of a letter? How would you know it was really someone from the IRS calling you?
A partnership K1 should be entered on the K1 Input form in 1120S, and it will flow thru to the shareholder(s).
Be careful with basis, but since it's a partnership, lack of basis isn't normally a problem, BUT you still need to track the S corp's basis in the partnership.
If an S-Corp owns a C-Corp, and the C-corp pays dividends out of retained earnings, then the C-Corp would issue a 1099-Div to the S-Corp, which would in turn issue a K-1 to the S-corp shareholders reflecting those dividends. I think that is what you were saying.
Here is a copy of a letter from the AICPA to the IRS asking for clarification to which the IRS has yet to respond:
https://www.aicpa.org/content/dam/aicpa/advocacy/tax/downloadabledocuments/56175896-aicpa-comments-erc-2-25-21.pdf