You lose permanent bonuses, same % as the rest of the stuff you do. You "don't lose" the ones you spent on Booms or Turns since those are already "spent" to make your country better, of which you're going to lose a % of anyway.

I can't say I've ever spent points in +Def Bonus before, that bonus is THAT bad, so... yeah. That bonus needs a massive buff or overhaul; currently it doesn't help netters, nor does it help warmongers.