@dank-cushions CDMage looks like some sort of disc extraction/manipulation tool. There shouldn't be anything inherently wrong with consolidating the .bins, but maybe it was done incorrectly. That's why we should see if the original files work before we start pointing fingers at the conversion.
But a single .bin or multiples shouldn't matter as long as the .cue is correct; as I understand it, they both represent the same raw binary data stream to recreate the original optical disc. I ended up with one when trying to apply the English patch to Rondo of Blood for the TG-CD, that worked fine (as far as I can tell. I've only played through the first level but it works at least that far.)
Before I knew that chdman would work on .iso/.wav./.cue sets, I thought you had to have .bin/.cue. So, starting with the multiple .bin/.cue set I:Burned the multiple .bin/.cue set to a disc. Re-ripped the resulting disc to .iso/.wav/.cue using TurboRip (the included binchunk tool that was originally meant to do this conversion gave a divide-by-zero error on Win10, and in compatibility modes for Win7 and XP.) Patched the resulting .iso/.wav/.cue set with the included instructions. Burned the patched .iso/.wav/.cue set back to another disc. Ripped that disc to .bin/.cue using ImgBurn.
This gave me a single .bin file. At first I was worried I had messed it up, but I put the .cue through chdman, dropped the resulting .chd in my tg16 (pcengine) folder, fired it up, and was pleasantly surprised when it worked just fine.