im not exactly sure what you mean - if you can be more specific, please do.
i know when my truck is going in for work, i always take out my chip if its going to the dealership; if its going to my regular mechanic, i tell him about the chip and i ask him if i need to take it out or if its ok to leave in for the work he wants to do. the problem with leaving it at the dealership is that theyll try to blame whatever they can on the chip and theyll try to charge you for warranty work as well claiming that all kinda of other stuff is messed up because of the chip.
from what i understand, if they try to pull codes, itll get all screwy with the chip in there. itll either spit out bogus codes, or no codes at all - whatever, i just know that they wont get anything accurate like that.
once you get your chip, though, youll see how easy it is to take out and put back in. mine usually takes me about 5 minutes or so, with 3 different size sockets and a toggle extension, which you may or may not need (plus the half hour to reset the battery, but you can go watch tv or something while thats happening.) its really no big deal.
i dont know much about the apten deal, but theres a lot of info floating around about it.