if they really wanted to, they probably could detect root...but we can unroot using adb or terminal emulator.
that being said...i will throw this out there as I always do: if you choose to root your phone, there are risks. if you brick your phone completely thats on you and you should have known what you were getting in for. i am completely against people returning bricked phones. pretty much everything can be fixed however, and too many people give up to easily.
motorola, htc, and other oems lock down their phones primarily because too many "geniuses" are returning bricked devices and they want to stop this. simply put if you root and mod your phone be prepared to eat the cost of it.