As they said (at least on their Discord server), EmuDeck won’t be deleting your yuzu.

Now that yuzu is dead anyway, I went ahead and replaced my mainline build with the latest early access build from Pineapple EA (afaik the repo is just some guy who compiled yuzu whenever there was a new early access build or something like that).

If you want to do that too, the AppImage should be in /home/deck/Applications, you just have to make sure the new one has the exact same name as the old one and that the new one is executable. Or you could also backup the yuzu AppImage from there if you’re paranoid.