You can just go ahead and transplant those two drives from your mk2 to the mk2a. You won't lose any settings, since all is stored on the disk(s). Just make sure to begin with synchronizing the software version!
The empegclone tool is just meant for transfering the mp3 files (?) and doesn't copy over settings and such (?). I can only imagine the clone tool to be handy when transfering the contents to a different size empeg (without 'transplanting' the drives).

Good luck!

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Edwin de Vaan