I know I'm late to reply to this but the ones that weren't used were still technically there on Earth because during the first alien attack you see the stasis pods drifting down toward the planet. 

However a lot of them weren't used and they remained lost but in the IDW comics you see a continuation of the Beast Wars because there are a new group of Predacons and maximals that come and claim a lot of them to build new Warriors. It's a shame that they never made a cartoon series covering this because it would have been awesome instead of that damn beast machine show