They'd be the one and the same, only different.
When Crono and Co defeated Lavos, they changed the future. The Lavos in 2300 AD was discarded to the DBT along with everything else in that timeline. But that was still Lavos. The only difference would have been that its physical body would have remained in the real world and had a different future (possibly decaying or remaining perfectly static). The Lavos in 2300 is a defeated Lavos (he is there because he was defeated)... but he is not the dead Lavos (who exists in the normal world).
As for why there is only one, that depends on the nature of time itself. If every change to the past produces an entirely new timeline, then either the DBT must be filled with countless Lavoses, or there must be a countless number of DBTs each containing one. Either way, there are too many of something.
If, however, time is elastic rather than brittle, then there would not be this problem of excessive numbers. That is, things aren't usually discarded to the DBT since they are minor disturbances; only when major distortions occur does the DBT come into play.
For more information on just what I am talking about, see this thread (this page, top post):
http://www.chronocompendium.com/Forums/index.php/topic,6845.45.htmlYou'll need to shift your paradigm, so don't forget to pop the clutch.
