To the best of my knowledge the second Watchtower and several other smaller annexes were still in orbit. My research barring re-watching has not shown any information about the fate of the second Watchtower.

I do know by the time frame of Batman Beyond the facility known as Watchtower was a building in Metropolis.

EDIT: In doing my research on Watchtower II's fate I learned this: The second Watchtower was fitted with extensive weaponry to defend Earth against extraterrestrial invasions, most notably a "binary fusion generator", a directed-energy cannon pointing down at the Earth.

Going to the Watchtower may be more beneficial, getting the weapons online could save a lot of lives before they are ever put in any danger at all.