But will it work or will the board not boot because without the port it will get an error message because something needs to connect through?
Don't worry, as long as the troubled one only those PCIe socket, It will work. Even I've wiggled the pins (PCIe 16X) a few times until they snapped off while I was facing the same problem with my old mobo, and that mobo still working properly after.
Which PCIe socket that troubled, by the way? (PCIe 16X / 1X)