yes they can, as an answer, but in what situations varies.
if you mean when you go in for a service, well they will have an incline depending on the garage and then obvioulsly if they drive it.
The next stage, ie if you are claiming warranty, well maybe not. again they may find errors or differences when they plug it in to the diagnostics .
However i remmeber a while back a couple of guys on the forums who blew up ECU's using old style chip tuning. Initally they were changed under warranty, then when the ECu got sent back to headoffice for the garages warranty refund, the fiddling was spotted, leaving the garage chasing the customer for a 800 quid ECu bill.
So moral of all this is ensure if you do go for a remap you are aware that your warranty will only be as good as the dealer is nice. technically you are voiding it, any claims after are pure bonus.