Hi,
Don't know if it can help, but I remember having that kind of issue with BotW when I went from SX to Atmosphere.
The game without any updates and DLC was running fine, but as soon as I installed updates and DLC the game crashed at launch, and my Switch told me it detected corrupted datas.
I tried many sources (my own game backup and other sources), many install tools without any success.
What I did to solve the issue, and in which I didn't believe it would work, was :
- Launch / get back to Hekate ;
- Before touching "Launch CFW", hold the two Volume buttons pushed to launch the Switch restore mode ;
- When in restore mode, don't touch anything and just turn off your Switch ;
- Turn on the Switch and try to launch BotW.
I read one day that just launching restore mode without doing anything else cleans residual / corrupted files / updates.
Worth trying I think.