I'm not the smartest bloke around when it comes to this stuff but I like to be prepared. I was just wondering if (or maybe when) I get pinged by the EPA for my life saving loud pipes would I have to get the bike retuned when I put the original pipes back on just for the test? Would it wreck the engine if i didnt? I dont think id be traveling more than 100ks before I'd put my life savers back on.

With a tune She would run a lot cooler, I wouldn't be riding to far without having her tuned.
Perhaps invest in a Auto Tuner if She's a EFI.

If it's just got the usual pipes and AC then it should be ok. As you say you only got 20km round trip and your not flogging it.
Plenty of bikes with pipes and ac that haven't had a map flashed and they seem to be ok but not great. Usually they are running a bit lean.
I would think if it's currently mapped for the pipes and other mods and you put std pipes back on it would only increase the back pressure and perhaps just run a little rich.

its just gona run shit, dont fang it and should be ok

Has he even got a turner at all? Maybe he's in rice bubble mode stage 1.

As I mentioned earlier, if it's only a stage one download installed, there won't be a problem. You may notice a bit of "run out of puff" up the higher rev ranges with the constriction of OE mufflers, otherwise it should be quite ride able. It'll probably be running at a good A/F ratio with stock cans on...LOL..You should have nothing to worry about.