Are you using BaseCamp at all? If so, you can do a backup, there. Then do your transfer and check things out. A restore will get you back to where you were with the Garmin, if you don't like the results.
I don't believe it will have any affect on the Garmin installed maps or POIs. It WILL overwrite any custom POI file you have on the Garmin device. What you need to do, is keep the custom POI file on your PC and update it with any additional POIs you want, then upload to the Garmin again.
2014 Allegro 36LA