There really should be an option to just change the core without deleting a re-scanning. This has always been an issue of mine as well.
I actually just manually edit the playlist myself but there really should be a more convenient option for this for the less tech savvy.
I think this could be handled pretty simply. One method could be just as simple as adding an option that just wipes the core selection in the same menu where you select cheats, add favorites, shaders, etc… Then you just relaunch the game and pick a core again.
Another option could be a little more advanced and actually show you the current selected core and allow you to just cycle through cores any time you want. Then you relaunch the game and it loads in the new core.
Either way, an easier method to change cores via the GUI is a feature that really should happen sooner than later.