I ran into a similar issue on a core conversion once. The product was a very weird one that we didn't anticipate ever offering again. The portfolio of that product was relatively small.
We went ahead and made the purchase and conversion knowing that each one of these loans would require some specialized handling each month until they paid off. Most of them were maturing within 4 years.
Once the conversion was made, we had officers reach out to each borrower and offer a better deal with a lower rate to refinance into a standard product the core would support.
We had a couple of customers that we had to sweet talk even further with some additional incentives and one who wouldn't respond to our calls or letters at all.
In the end, after a few months, only one was left on the books and it still required special handling every single month.
My advice, find some way to work with the customers to refinance or change the documents so it will work on your system.
Bought a new core system that can't support this product as it is designed.
And tell them not to do this again.