It's a slippery slope and AC is wise to ignore unproven claims of missing, undocumented cash, especially when other airlines, security, and customs are in the mix as posible supects.

If not then next time they may be on the hook for $1000, or 10,000, or more. In this light losing the OP's 40k of airfare is a small price to pay, especially as people would try to game the system if this becomes a loophole. This loophole must remain closed.

Good decision by AC to not be held ransom for random cash claims.