the interest due on their loan is now greater than their regular payment amount.
Sooo... what's going to happen when you receive the next full payment? With more accrued interest than payment, will your loan servicing system pay the interest by negative amortization? Is that legal and consistent with the terms of the promissory note?
I concur with Randy's advice to involve legal counsel, but suggest you take this one step further. Using this case and counsel's opinion re proper handling, add (or expand) this topic to your loan servicing policy and procedures. If other prepayment situations also happen from time to time, take the time now and write it all into procedures--that way, there will be no guessing (or costly mistakes) in the future.