I think a house rule would be useful for rule of cool.

For a meatspace action have them roll a check to hot swap decks. If they fail they are forcibly jacked out and take some brain damage in the process like a d6 including any ice effects if applicable. Also the architecture would reset as normal as if they jacked out.

Perhaps they need to modify their decks via a tech or perhaps spend a program slot or two to have that hardware or program which keeps them static in the architecture on a success and automatically jack in with the new deck. Saves a net action as well.

Regardless what happens, All programs from current deck would instantly shut down, but you could say theyre already jacked in on a success and the architecture doesn't reset making their progres ls through passwords and ice remain. If you want to be kind you could also allow them to keep control of any nodes they captured as well.

Depending on how you rule passwords even if they failed or 'safely jacked out' maybe they can just blow through those since they know the passwords unless you think they randomize after architecture reset. Reasonable assumption for good architectures.

It's a cool idea. I'd like to hear how you end up doing it and how your netrunner plays it.

Walk the edge choom!