I am almost positive you will have no problem doing it online, if not, by all means insist at the airport, if you have to clear immigration/customs go out and then back in..............I can almost assure you , that you are toast. '
The lines are not long but you could easily wait 20 mins for your luggage, by the time you are out and back at the check in counter the copa flight will be , almost for sure, closed.
But again, I am 99.99% sure you wont have a problem.