Its kinda obvous, things like neos fragments, we cant use them because the collectors wont take them again but for the player driven events they are still a great tool but your S.O.L. if you got rid of them all, or ever never around to collect the items in the first place.
Or maybe even things like the red or blue pill that you sometimes get in those missions, I mean even if they didnt do jack, just the animation and icon would be a great plot device.