kind of reminds me when i tested the 64GB emmc deck with bazzite ages ago. it would not shut down properly, but it was plagued with so many issues besides shutting down improperly
btw i dont have a fix. i would make a #bazzite-help thread if it really bothers you or make an issue in our tracker on github. this isn't too bad of a workaround though. next time you want to update, go into desktop mode > open the System Updates application and shut down from desktop
when it comes to suyu i would wait until get get accustomed to the code more, right know i would imagine they are trying to figure out the code and would consider it unstable. can instead use archived versions of the old program
im using archived yuzu until ryujinx becomes the faster option while keeping an eye on suyu development for citra you can use pablomk7/citra (named ññ now ) also keeping an eye on a different archive that seems to have gotten the ci working again