Chrono Cross still used it. :3 (Yes, there's a functioning Enertron in the game. ^_^)
In fact, Chrono Cross was pretty well cross-referenced with the first game's translation. The only gaffe in the whole thing is Guile, who was Alfador in the Japanese version - a subtle clue to his on-again, off-again true identity as Magus (Alfador was the name of Janus' cat, remember?). But then, it's arguably the programmers' fault, not the translators. Chrono Trigger DS even reverse-imported one name from Chrono Cross: the Gold Gemstone's Triple Tech was originally Grand Dream, a reference to the Grandleon (Masamune) sword that Woolsey apparently didn't think to change. The name Grand Dream (Grandream?) appears again in the Japanese version of Chrono Cross, a sword created (IIRC) from combining the Grandleon/Masamune swords from the two alternate timelines, but the U.S. version gives it the more appropriate name of Mastermune - hence the DS version of Chrono Trigger calls the Triple Tech Mastermune as well.
...To be honest, "Masamune" is the only name change that I don't think was a marked improvement over the original. "Mash, Bash and Gash"? That's almost as bad as "Dog, Mag and Rag" (better known as Sandy, Cindy and Mindy, FFIV and FFX's Magus Sisters, no relation to Magus himself XD). The thing that I find clever in retrospect? Melchior, Balthazar and Gaspar have the exact same initials as their Japanese counterparts. I mean, what are the odds that a famous trio of wise men existed in history whose initials matched up perfectly with a trio of fictional wise men in desperate need of new names?