Story thus far: Digital copies of Pokemon Sword/Shield will delete your Switch's data, forcing you to redownload all your games and it's updates.
Save data seems unaffected, however this affects your Switch's NAND which can cause issues reading game cartridges and potentially brick your console.
We thought it was related to autosave but that's not the case, it can happen to anyone.
Links:
https://twitter.com/DeathChaos25/status/1195207032531554304https://twitter.com/kirihiiro01/status/1195142836452130816?s=19https://twitter.com/rubidium1116/status/1195180255893311489Japanese twitter tag: セーブデータ = Save Data
https://streamable.com/4hj9aRemember to say #ThankYouGameFreak for deleting your games, anyone who thinks they should keep their data is entitled.