Belthasar's Neo Epoch, as well as Belthasar himself, were still in Viper Manor just right before you visit Terra Tower, because I specifically went there to visit him, to see if he'd tell me about the Chronopolis vs. Dinopolis war. I wasn't too far off, but I had to wait for that scene in Terra Tower.
In which case, Belthasar probably didn't even actually set foot in Terra Tower.
Most likely, it was Belthasar communicating with Serge's consciousness telepathically. Like Kazuki said, the scene of Viper Manor in Terra Tower wavers about, as if in a dream state, so I think that backs it up pretty well. After all, Belthasar tells Serge, "This is a space that doesn't exist."
My question is, why does Terra Tower transform into some bird-looking totem-pole-esque kind of statue after defeating the Lunar Dragon? You can't even go back inside Terra Tower after that, so why doesn't the bloody tower just explode or break apart altogether? Which significance does its transformation have?
