That's never come up in my games because leveling is always done during downtime when players have access to fabrication between missions to reconfigure their mechs. I would suggest if you end up with a situation where they don't have access to printers but may find parts and upgrades some other way (which it suggests is rare but can happen on page 43), I'd probably let the players apply apply their bonuses by "reconfiguring" the existing frame just to let those bonuses keep up with other upgrades.