Just try replacing one and seeing what happens. I don't foresee it being an issue, since the oggs most likely came from the soundtrack in some form or another anyway, so the loop points -should- still work with a re-encode. It's not like the tempo is changed or anything
Failing which, might be possible to open up Audition to line up the CD version with the existing ogg before encoding, since unlike MP3 encoding, ogg does not add silence to the beginning, changing the timing.
Failing which, might be possible to open up Audition to line up the CD version with the existing ogg before encoding, since unlike MP3 encoding, ogg does not add silence to the beginning, changing the timing.