I guess Bulma rebuilt it to suit her needs, I dunno. Only the anime has the time machine being destroyed so far, so a quick and convenient way to explain any plot holes is that Toriyama didn't actually write that part and that scene was the anime writers expanding on his notes.
Since that time machine was the first one to actually travel to the main timeline (1 year before the mecha freeza saga), my guess is it always just travels back to the main timeline when used to return to the past. The real question is why it travels to Trunks' future rather than Cell's, but like I said, probably the anime writers' fault, or just plot convenience since Cell's timeline is unimportant to the story.