I make EmulationStation only display .cue and .m3u files. That works great to show only one entry for each bin/cue pair. For multi-disk games, I create an m3u file that points to renamed .cue files. I change them to something like .cu2 so that EmulationStation won’t display them. Then you can sway disks in the RGUI.
I was wondering if this would work in EmulationStation! I have done this previously on the Openemu app on osx. Same thing, you create a .m3u playlist file that points to each .cue file (which in turn point to their corresponding .bin files). This allowed multi disk switching through the GUI. I’ve only started using a Raspberry Pi and Retropie but I’ll try this out! If it works it should probably be a pinned post, as there will be no need to convert any bin files into pbp’s.