Quick and Clean Atmosphere Re-install
I am aware of several homebrew apps that come with modified atmosphere files in their zip packages.
Those modified atmosphere files will break your atmosphere install esp the controller in the homebrew apps and some of the games.
If you want to run clean/fresh Atmosphere
follow these steps
1. backup your Nintendo, switch and emuMMC (if you have this folder) folder on your sd card to your pc.
2. delete atmosphere, sept, and switch folders from your sd card. delete hbmenu.nro file from your sd card.
3. download the latest Atmosphere zip file and extract to the root of your sd card https://github.com/Atmosphere-NX/Atmosphere/releases
4. download fusee-primary.bin, this is the payload you will use to boot your Switch. (It will go in your tegrarcumgui, on your dongle, on your phone)
5. download Sigpatches from here and extract to the root of your sd card. - this is optional for some of users.
6. copy your Nintendo, switch and emuMMC (if you have this folder) folder back to your sd card and put your sd card back in your Switch.
7. get your switch in RCM mode then inject fusee-primary.bin
8. Hold R while tapping the Album Icon to enter the Homebrew Menu - for full ram, Hold R while tapping one of your games to enter the Homebrew menu with full ram.