I also think this is really interesting.
I think I would go to the store first, with the idea that they need to honor their voucher, even if it costs them money due to some kind of confusion on their end. The point is to actually obtain a turkey dinner, or equivalent cash/store credit, right? So if I go directly to the store and I obtain my item, I don't necessarily care who the "turkey thief" is, or what investigations happen behind the scenes after I leave.
If the store won't honor the voucher in some way, then I think I would need to go to the church, and explain that I either need another document the store will honor, or I need my auction check back. Whichever is easier. And again, once I've got my item/money, let someone else sort it out behind the scenes. (Although personally I would be VERY curious to know what was going on!)
For me, $50 is not make-or-break money, but it is too much for me to just write it off.