It is definitely unusual. The WSOP did it out of pure necessity (AFAIK). That's what happens when you go from 800 players to 8000 in 3 years.
You could run 3 separate tournaments (3 tournament files), saving each at the end of each "segment" and loading the next one. Then combine them manually at some point by creating a new tournament with the remaining players. Of course, you'd lose tournament history this way.
I guess you could have all 60 players in one tournament and then handle seating manually. You could drag the current players to their seats if you wanted the TD to display the seating chart accurately, but you couldn't let it automatically balance the tables, because it would simply tell you there were not enough seats for everyone.
I don't think either of these scenarios is ideal, but then the TD wasn't meant to manage this scenario. Sorry. If I were running this type of tournament, I would probably use the second method and move players myself. Of course, if you're also playing in the tournament, this will be more challenging.