Backing up Ryujinx/Switching EmuDeck to the Flatpak version of Ryujinx
Method A) Using and Backing up the Flatpak while you can
As of the time I'm writing this post, Ryujinx can still be downloaded from the Discover store/Flathub. Go download it while you still can, then run this command in Terminal/Konsole:
This will drop "ryujinx.flatpak" in your $HOME/ directory or "/home/deck/" (if you're on a Steam Deck). You can just double click this file, and Discover should open up and prompt to install.
Simply building a bundle won't include or scan whether you need to download dependencies. This method detailed in Flatpak documentation will achieve that, though I have no experience with it. Despite its name, you do not need an external USB drive. Skip any steps that tell you to mount/unmount a drive and replace the "drive" directory with whatever directory you want your flatpak to go.
For what it's worth, I simply built a bundle and used it to install the Flatpak on a fresh Linux Mint install, and Ryujinx worked with no issues.
We need to make a manual changes to Emudeck in order for any of the Steam ROM Manager entries to work with the Flatpak version of Ryujinx. This should not break anything major, but may actively need to be updated/repaired when EmuDeck needs to update. Maybe the EmuDeck team will fix their script's functionality at some point in the future to help maintain compatibility the same way that they do with Yuzu.
You need to go into the drive you installed EmuDeck > Emulation > tools > launchers > Open ryujinx(.)sh with Kate or another text editor.
On line 4, you will see
you need to remove the .sh from Ryujinx(.)sh. It should now read
save the file.
EmuDeck does not technically know that Ryujinx is installed, as it uses the Binary version. However, with this change to the launcher script, any entry made with Steam Rom Manager will search for and use the Flatpak version just fine. The reason you have to make this change is because by default, the script tries to find the Flatpak version if the binary version is absent, and the variable (emuName) would not work properly if it's searching for a Flatpak with the ".sh" extension within its name.
With this method you also need to use Ryujinx's default folders to put the title/prod keys in, rather than the ones generated by EmuDeck. Open Ryujinx, go to File > Open Ryujinx Folder > system. Place your keys here.
Method B) Backing up your already existing EmuDeck-installed copy of Ryujinx
This is a lot more straightforward and (until/unless EmuDeck gets updated) hassle-free, provided you already have Ryujinx installed via EmuDeck. All you need to do is go into $HOME > Applications and backup your "publish" folder. Everything in that folder. I just right clicked > Compress > publish.zip.
You can also backup your settings by booting Ryujinx > File > Open Ryujinx Folder > backup everything in there.
Next time you need to install EmuDeck, copy everything back into $HOME/Applications/publish and EmuDeck should work as if it had installed the Binary version itself. You do not need to modify the launcher script as in Method A when you do this. You can continue to use the EmuDeck-generated bios folder to place keys. Only real difference is that Ryujinx won't show up in the Applications/Start menu.