No worries! It’s totally fine.
The /atmosphere/contents directory has things like your system modules (themes and stuff) in it.
System modules often break things when you upgrade Atmos/FW so it’s common to tell people to delete them.
I like to keep a backup instead of deleting so I can move the modules that work back and identify and download updates of the ones that don’t work.
No big deal.
thanks a lot! the games are working again, seems to be cos of the sigpatches. but tinfoil still won't open, no matter how many times i try to delete/reinstall