Not on a given Citra installation. Since the 3DS didn’t support something like that, Citra doesn’t either as we follow the 3DS’ file system. You can set up a portable Citra build (with its own configuration and save files) specifically for another save game:
Go to Download Citra - Citra and select Manual download. Then under Nightly Build, click on your operating system’s icon to the right of the latest build available to download the build.
Extract it (.7z can be extracted using Winrar or 7zip) and put it where ever you wish. Inside the extracted mingw folder, create a folder called user. This Citra should now store all of its config, save files and such inside of this user folder.
Check to make sure that this user folder is in the same folder that contains citra-qt(.exe)
Now run the citra-qt executable found inside of the mingw folder.
Yes, but it’s not through Citra and there’s a chance it may cause issues: you just have to find your save file and make it unreadable to Citra somehow (best method being to put the contents in a zip folder or the like so you can unzip it and play on it later if you wanted), then Citra won’t be able to see any save data and you can play it without your old file being recognized.
So that means if I put Touhou Island in a zip folder then grab a new Tomodachi Life game, it won’t effect Touhou Island and I can always get Touhou Island out of the zip file and put the second TomoLife game in the zip?