Now, all my games are gone, and the N64 console is missing from the options.
The Update does not delete any games.
But it is not possible to upgrade directly from version 6.1.1 to version 8.0, it was necessary to reinstall the system.
Do you use an RPi3 then? Rpi3 is not strong enough to emulate the N64 (nor dreamast and PSP), if you overclock it you will be able to run some games better, but even an Rpi4 "suffers" to emulate the N64 (but many users claim that overclocked the Rpi4 runs well on N64 and Dreamcast - I don't have Rpi4 so I can't say for myself).