second endorsement check accepted by bank

good day to all
i'm employed to a private security company and i want to ask advices regarding to this situation:
during payday there are some guards still not having their atm account for their payroll crediting, therefore their salary will be in form check issuance.
checks then forwarded to operation assistant for the mailings of checks, unfortunately one or several checks where missing.
after 3-4days it was found out that it was debited to the company account and also found out that it was deposited thru other bank (bank to bank transaction) and it was secondly endorsed
questions are
is there a way recover the amount to the bank since it was a second endorsement?
what are possible remidy?

thanks in advance