You will have to manual change the IRQ of Com2 in your BIOS. But your hardware and software will have to support the change.
Com1 and Com3 use the same IRQ (4) and Com2 and Com4 use the same IRQ (3). While each has a different base I/O address, you will still need to change the IRQ in your BIOS.
Normally IRQ 2/9 (they are the same), 10, 11 and 12 are open. So if your MoBo allows it, you should be able to change with (hopefully) no problems.
Hope this helps.
You could say I've been around.