Both Yuzu and Citra are still available on the Discover Store, or at least they were when I checked ~12 hours ago. I don't think Emudeck will uninstall it, they certainly aren't required to.

EmuDeck is already implementing replacements on Switch and is looking at other 3DS emulators. They won't uninstall Yuzu from your Deck, but likely won't default to using them if they're installed. You might have to take a few extra steps with ES-DE or SRM.

I'm probably just not going to update emudeck. All the games I want to play already work fine so I don't see why I should

It's honestly too soon to tell what the future might hold.

Many people have already forked the project, downloaded it in advance, created installers that do not require internet access.

Perhaps holding off an updating is smart for the moment. But we have to wait and see what happens when the dust settles. If you got something that works right now, just be patient.

The devs behind Yuzu/citra were required to take down the repository's, but this doesn't mean anyone has to uninstall those emulators.

Because the projects were open source, Yuzu/citra will continue on under new names most likely (Yuzu is already available as "Nuzu" for example).

So eventually emudeck will probably switch to providing the new Yuzu/citra once it becomes clear which revival project is going to be the most popular.

Emudeck removes Yuzu and Citra support https://www.gamingonlinux.com/2024/03/emudeck-removes-yuzu-and-citra-emulator-support/

Retrodeck update : Yuzu and Citra removal https://retrodeck.readthedocs.io/en/latest/blog/2024/03/04/march-2024-tiny-update---yuzu-removal/

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.