Do check
@Doctorbeefy's solution first as the fresh Atmosphere/Hekate install might not be necessary.
Are you on latest Atmosphere/Hekate/sigpatches at all? If you're not on firmware 17.x.x, did you clear your prodinfo at some point in the past?
if you're on the latest version of Atmosphere/Hekate, you can follow
this guide which will give you the latest Atmosphere, Hekate and some of the homebrew apps set up. Additionally, you'll need the latest
sigpatches (in order to run games) and
DNSMITM (to block Nintendo servers). Before deleting those other folders, I'd make a backup of them as well, just in case. You can probably restore your apps from the switch folder, provided you know which one of them aren't causing the issue with the game (I'm not familiar with mods, unfortunately). You might have some custom .ini settings set up for your Atmosphere/Hekate, which you can restore later from the folders you've made a backup of.