Now we see him riding it away from Burmecia at the end of Disc 1 and away from the Iifa Tree at the end of Disc 2. However, he then seems to start using the Hilda 1 as his mode of transport (presumably because it can hold more people =P) and we don't see the Silver Dragon again.

...that is, until the tri-boss fight with first the Silver Dragon, then Garland and then Kuja.

However, what is there to say it was Kuja's Silver Dragon? After all, it was seemingly commanded by Garland and if it was Kuja's, then Garland would have been aware Kuja was on Terra.

Now if it was Kuja's Silver Dragon, I dunno how it got back to Terra in the first place or what happened to it after Disc 2.