At least on the NOOK Color, if you remove the uSD used to boot the N2A card, they have no way of knowing that you ran it. I believe the same is true on the NOOK Tablet, but I am not 100% certain.
Under normal circumstances, there should be no danger of doing any sort of damage to your device that would affect B&N's warranty unless you are really determined to do so. Do be careful with anything that loads to internal (eMMC) memory. Some people running N2A cards and the like have installed ClockworkMod to eMMC, and have had OTA updates blocked. That B&N can detect.
You have to realize that B&N consider anything but their own firmware competition. They want your money, and feel that your purchase of their device entitles them any of your money that you spend on media. Whether you're happy with that arrangement is up to you.
I agree with the previous post. My daughters are each running N2A cards on their nook colors. You pop in the card and the system boots either under the Nook side which remains untouched or switches to running completely on the card. The two sides do not "speak" to each other. There is no way to even access files on the Nook side from an N2A card and vice versa. As soon as the card is removed, there is no evidence that N2A was present, ever. All the files it creates stay on the card. Even with the card inserted when you boot on the nook side you can't tell that N2A is present. N2Acardsdotcom explains it very well. I would highly recommend getting one. Makes a mini ipad for $35. My girls can do nearly anything I can on my ipad.
It's also possible that the person you spoke to doesn't really understand what an n2a card is/does. Many people assume it roots the Nook (messes with it's internal memory) rather than simply running something on top of it - kind of like wearing a mask (n2a) vs. cosmetic surgery (rooting).
To put it simply, when you have the N2A card physically installed in the device, you can choose to use it--off the card--OR to use the native software. Take the card out, and there's just the native software, nothing altered. It never touches anything, No way to know it was ever used. It does not invalidate the warranty.
Unfortunately NC has limited storage for apps. I hit my limit, so I got the N2A card which allows me to purchase a LOT of apps from Android Market. I have to rotate the B&N aps when I use stock. I can only play B&N apps in stock. I power down and re-boot into android to use all the rest of my apps.
The N2A card does not damage the NC stock in any way. It only utilizes the processing power of NC to run the non- B&N apps off of my N2A card.
For practical purposes, think of the Nook and N2A card as two different devices in one package. The N2A card is a complete operating system, it is not additional storage for the Nook such as a standard blank SD card would be. These are the rules for access between the Nook and the N2A card:
The Nook can only access the storage on the Nook, it cannot access any of the storage on the N2A card.
The N2a card can access the storage on the N2A card, but it can also access the storage on the Nook.
I had a bit of trouble with the concept in the beginning as I too wanted to use the N2A card as storage for the native Nook. It helped me to reverse what I normally thought regarding the Nook and the SD card. Many of us don't even use the native Nook interface anymore, so in effect, the Nook storage becomes extra storage for the N2A card. In other words, the N2A card is our operating system and the Nook storage functions as an SD card for more storage.
One common way of moving files between the Nook and SD card is done by booting into Android (N2A) and connecting the device to a computer with the power/usb cable. Two new drives will show up on your computer. One will be the Nook and the other will be the storage on the card. Just move/copy files between them as you would any two drives/folders on your computer. This will work for any files on your Nook except for Barnes and Noble content.
If you remove the N2A card from the NOOK SD Card bay, there is no trace left behind tha the card was ever there. How could that void the warranty?
as it is a micro card how would they know. i have 2 nooks and both ahve the n2a card in them. one went back for repair no problems. just remove the card b4 you send it back or take in in. b and n has no way of tracking this item. it works great.