The auto-USB copy function has historically only copied NEW files from USB to Pi. It would go through the files on the USB stick and copy over anything that wasn't already on the Pi. You don't lose anything on the pi.
@mitu I loaded retropie onto the sd card, then rebooted. then I started back up and put in the USB to populate it with the folders. Then took it to my PC and added all the roms. Then plugged it back in. So no I am not running them off the USB. I just didnt know if I plugged the USB back in to add more roms, with the original roms removed, if it would remove them from the SD card
The documentation got you covered - https://retropie.org.uk/docs/Transferring-Roms/. About the SD card - the Linux partition where the actual system is stored is not visible in Windows (just the boot partition), but there are other methods for transferring ROMs, oulined in the docs.
Note that selling systems with RetroPie pre-installed is not legal and support for 3rd party images is something that's not the topic of these forums.