Several possible answers:
1) Mark the bats you find illegal. Check for the mark.
2) Ask to see the "other" illegal bat (the one you disqualified). If you can't find it, rule that the bat the batter has is the one you disqualified.
3) Put the DQ'd bats in the trunk of your car (or other spot out of the reach of the players).
4) Ask the coaches what they'd like to do -- after all, they are the customers and the customer is always right.
5) Allow the bat, but report the incident to the state (or to the association so other umpires can watch for it).
6) Don't check the bats in the first place. That way, you don't have this problem.
7) Don't check the bats as the players come to the plate. Ditto.