The way it sounds is that it actually just resets the counters. So if you go and use Hastega II -> Predator Claws, then using Apogee will simply reset both BP cooldowns from their current timer to 0. It won't preserve the previous one, it will simply reset the timers. It still has more potency then current Apogee, especially if the MP cost boost is removed, because you can now get in four pacts in a very short period whenever Apogee is up as opposed to three, with no additional cost if their plans go through.