You should order a stop payment on the check and either cover the fee yourself, or tell the tenant you are deducting the stop payment fee from their refund, since they were at fault for losing the check. You can then reissue the check without having to worry there are 2 checks out there. And yes, you are still legally required to issue a new check or otherwise refund the money - a glitch like this does not negate your obligation (same thing as if the check was lost in the mailed, ruined by water damage, etc).
Good luck.
