A customer sent a cashiers check to a vendor and the vendor lost the check. Given it has been less than 90 days we were unable to replace the check so the customer paid using a different method. Once the 90 days is up can we give the remitter back the funds instead of replacing the check to the payee?

You can give the funds back to the remitter whenever you want to, but if the original check is ever properly presented, you are going to have to pay it regardless.

The vendor (who lost the check) can provide the appropriate affidavit of loss, theft, or destruction under UCC 3-312 and make a claim. That claim and affidavit would allow you to refuse payment of the original cashier's check if it's later presented for payment and, after 90 days from the original check issue date, pay the claim.

Your customer doesn't have a valid claim under 3-312, because they didn't lose the check.

Of course, because your customer paid the vendor after learning the original check was lost, the vendor doesn't have any real incentive to provide the affidavit and claim.

I suggest contacting legal counsel to see whether, if the vendor does make the affidavit and claim, whether the claim can be assigned to your customer so that you can pay your customer instead of the vendor.

Otherwise, what Randy ^^^ said.