I'd recommend finding a way to prove that your ink cannot migrate through the film and onto the product, either through internal testing or via a third party testing facility. And of course, have it documented along with a risk assessment. I can't help but think of the recall Nestle had when ITX was discovered to be leaking (migrating) into one of their products through the packaging. You may also be able to get proof of lack of migration through your ink supplier.
If you cannot prove that there is no possibility for migration with your current inks, it may be best to switch to inks that are approved for direct food contact.