In addition to this, any of your ships in the sea zone when the combat are presumed to have taken place in combat. The only way to avoid this is to move them during combat movement (even if the move does not result in combat).
Marsh
If Japan takes Calcutta and India retakes it, does it go back as a normal capital and receive ipc’s like it did before (minus the reduced factory)?
Yes
Just FYI it also ejects any Allied control markers (so if the USA controlled Shan State because you did not have a capital at the time, as soon as you liberate, the USA marker is ejected and it returns to UK control).
This is true of Paris too, so it resets all blue areas back to French ownership upon liberation if they were “liberated” Allied at that time.