Nintendo and Pokemon Co. could be in for a huge headache with the digital release for Pokemon Sword and Shield. It seems that some users are experiencing a rather nasty issue that ends up corrupting microSD card data. Save files are stored on the Switch itself, so your progress in all games will be fine. That said, it seems the corrupted microSD cards might need to be wiped, and you'll have to redownload all games.
While not specific enough to track just yet, it seems Pokemon Sword and Shield crashing is causing this issue. In other words, any crash you encounter could end up causing this problem. It would be a nightmare if save files were lost, but even without that being the case, this is a pretty cumbersome issue.