I've heard that they did, which is a shame (it's a great song) and really strange because not only is the location in the game but the song itself appeared in Alternative Saga so Falcom is presumably aware that it's sort of popular. Hopefully all the 'lost' tracks will get rearranged as bonus pieces on the OST or on some later album. *crosses fingers*
Thanks for the link to the uploaded music; I've only listened to a few of the pieces but so far I am underwhelmed, at least by comparison to Ys Chronicles, Seven, and Felghana. The version of Dawn of Ys is pretty lacking compared to the original Duo and Ys IV Perfect Versions.