I did some testing, and it turns out the GUID of commands is regenerated every export. I'd assume when exporting commands referencing other commands, the export updates the referenced GUID so it still works, which can't happen if you're only exporting the referenced commands.
To prevent mismatches, you'd have to export referencing commands as well, so you can import them again, together. Of course, this will prevent modification in the interim, so it's hardly a solution.
Alternatively, if you're just switching between sets of keybinds, while it's not as "neat", you could have a check in the commands themselves:
Begin Text Compare : [StarCitizenVersion] Equals '2.3'
Press A key and hold for 0,06 seconds and release
Else If Text Compare : [StarCitizenVersion] Equals '2.4'
Press B key and hold for 0,06 seconds and release
Else
Press C key and hold for 0,06 seconds and release
End Condition
I'm assuming you have a "setup" command that runs on profile load, within which you could specify which version you're using.