[Mikerochip]

Yeah, I understand.

Why TOSEC persist with that stupid split track setup I don't know.
(It's not representative of an actual CD. Or well, not accurately representative enough)
(Which is the whole reason Redump.org and TruRip etc exist)

You can create a new CD from the individual tracks that doesn't even remotely match the original, so, why bother with it.
Everyone else has moved on to whole disk images (Where this wouldn't be a problem).

Anyhow!

Use ISO Buster again,
once you do the above: create the new single .bin file with both tracks,

open the new .cue file in ISO Buster, and select each track one by one:
Right click on it, "Extract Trackxx" --> then select "Extract RAW but convert to user Data .iso" or similar.

(Since, I assume, the old tracks were 2048 sector, and in the new .bin, tracks will be 2352 sector tracks)

Do the hashes match?
(I presume they will, but, you'll have to try it)

You can automate ISOBuster, but, I've never bothered since every time I want to use it, it's a specialist job I have to do by hand anyhow.

Well, WinUAE supports .chd files since forever (thanks!!) so, using it shouldn't be a problem, with emulation anyhow.
Not sure if FS-UAE supports it or not.

And, if you want to burn the disk image, a simple:

chdman.exe extractCD -i "path to .chd" -o "path to new .cue" -ob "path to new .bin"

And you can just burn the new .cue file to a CDR, using a DAO mode or similar, depending on your software.
Most CDR burning software has supported DAO modes since around 1998 ish, so, it'll be hard to find one that doesn't support it!
Usually it's enough to just point to the .cue file and burn it.

(And remember kids, the speed you burn the CD-R at makes *no difference*. Slower burning (1x-4x) will result in an almost identical CD-R to a 24x burn speed CD-R, it will just suck up more of your time.
That piece of disinformation has been around since people had cheap shitty media with worse burners and woefully slow PC's)