There can be so many reasons why Atmosphere crashes.
Usually it's caused by different versions of the software and the initial payload.
Also 'old' stuff on your SD card like themes and stuff can caused problems.
I don't know how old your previous version of Atmosphere was but a lot of things changed.
I would recommend making a backup of your SD card (especially the Nintendo folder)
Afaik, you can delete everything from your SD card except the Nintendo folder.
Go to
https://switch.homebrew.guide/ and follow the steps overthere.
If you are on a Mac, note that OSX sets some flags on files/folders on your SD card which might also give some problems if they are not correct