Does a new game on PC, with mods enabled, load ok once synced to the Switch?
Try clearing the system cache: in the Home menu open System Settings, then select System, Formatting Options, Clear Cache and then the current user.
Note that this will also reset the system language and brightness setting.
If you start the game from a different user account, if available, can you start a new game and enable mods without crashing? A different account would give a separate drive space for saves.