Obviously they're not going to do the system in such a way that everybody immediately shoots to the top of it on stored stuff; that would mean they did all this work to build a system everybody will immediately bypass. That's not healthy for the game. It's the same reason you don't accumulate XP once you hit the current level cap.
Perfectly reasonable, they just need to give us an idea of where that cap will be. If it's 100 chips, and you have 400, you can go buy Mk XI gear for your BOFFs, or some extra DOFF Borg, trade for DIL, etc. TELLING the players roughly where that line is (even if we don't get all the math) lets us spend it however we want, since we earned it. Just having the 'extra' get deleted is how you piss off the players for no good reason. Understand the need for a cap, just show the players where it is.
Other side of the coin, if the cap is 1000 chips, the guy with 400 doesn't have to really worry about burning them off, and can spend a few and just let the rest convert, and he's then got some built-up value in the new system.
NOT telling people what's going on is where the angst and rage comes from. And if they're not smart enough to figure that out after doing it a couple times, we're in a lot more trouble than we think. I try to keep operating under the assumption that the DEVs aren't ACTIVELY trying to screw us over, so why would they be opposed to helping us through the transition smartly rather than keeping it a mystery, flipping a switch, and having people pissed off again?