As a jury-rig, I use the 'Refit PDC' command to refit one to itself - though I hardly ever repair PDCs. By the time they take damage, I've already lost the fight.
I don't know of any way to repair PDC armor other than SM mode. You could use the Repair All button on the F6 window and the SM Mods button on F2 to remove an appropriate amount of minerals and wealth.
Might be a silly question. . . . how do you repair PDC's? In the afore mentioned One Planet War my PDC's got badly dinged up. I've fixed the internals with damage control, but the armour has gaping holes. . . Poking around it doesn't seem to be a shipyard job, and there's no mention on the industry screen.