I did this several times while installing everything (moving from exFAT to FAT32 and back). Every time I would just copy all files in the SD card to my (Linux) laptop, format the card, and copy the files back. Never had a problem with that process.
I recently got Atmosphere running on my Switch and am now running some games installed from NSP files. Some of them pop up a window saying there is a game update available (but I can still bypass that and run the game). Is it safe to install those updates?