Are these games that don't show up card 2 games? (the list is on the first post). If not, then rename it to be as simple as possible anbd avoiding special characters.
First Page; you''ll see that La Noir doesn't work regardless of whop dumps the file, this is an issue of compatibility with SX OS, same as 1-2 Switch crashing the system on the eating game.
Your info is either getting corrupted, or the SD card has an issue. Either backup your license file, reformat, and try adding everything back to it, ONE BY ONE, or try a new SD card. This issue only happen when files get fragmented or the SD card controller doesn't communicate properly with the Switch.