Just like any new console that launches there are always a few wrinkles to iron out in the new system launch window. The Nintendo Switch was no exception with Joy-Con’s not syncing properly, Wi-Fi issues, and a weird bug that makes some very odd noises. It looks like there is a new problem that some Switch owners are reporting and that is the actual system warping if docked for too long. It is only a few cases that have been reported at this time so if you do dock your system for long periods of time maybe look out for it.
Your save progress is saved on the handheld unit so if you were to send it back to Nintendo you would most likely lose all your save progress. There are also reports of the docking station scratching the screen of the Switch so you might be better off docking it only if you really have to. Nintendo has not yet responded on the units that have apparently warped in their docking stations but hopefully they will swap them out if the warping gets worse.