The partnership should have filed a PA-65 for any year that they EITHER had PA source income or had PA resident owners for this partnership. That is fairly clear in the "Who should file" section where it seems the partnership meets both the requirement to have had activity within PA during some years AND had PA resident owners. So, if they were PA residents the entire time this partnership existed since 2012, then the partnership should have filed for all of those years and should have also included either schedule RK-1 or NRK-1 depending on PA residency status.
It may or may not affect the personal return because PA rules for some deductions differ from the federal, and I am not sure how you would have addressed that without filing the PA partnership returns and allocations of income within and without.
Did the partnership register with PA to do business within the state? Hopefully this isn't going to be the opening of a giant can of worms! I can tell you a horror story from my earlier days in practice, not me personally but the firm I worked for. I am also on the border of PA, just west of Wilmington, DE, and I also have clients from all the surrounding states.
I'm curious how this came up. I'm sorry, is it because former DIL has a new preparer for 2023 that asked for the back year returns?