"... it's a guess as to which software version to send ..."

Of course it just might be possible to label either the board or the programmed µC in such a way that one can unambiguously distinguish between the two versions. It also might just be possible that a customer you trust enough to replace that part could actually read this label and order the correct part, taking out any guesswork on your side.

As for maintaining and testing two (or even more) software versions, I'm usually not for it either.
However in this particular case the only difference (if the software is well designed!) should be between something like:

#define SYSCLK 11

and

#define SYSCLK 22

So all that's needed is to compile once for each defined frequency, giving two different HEX files. That's hardly the stuff of version control nightmares.
Testing has to be done twice anyway, so there's no difference there.

Needless to say that all this could have been prevented if some thought had been given to this problem before the hardware design had been completed ...

Regards,
Rob.