In the last act of Captain America: The Winter Soldier, this conversation is exchanged.
[Computer] Retinal scanner active.
[Alexander Pierce] You don't think we've wiped your clearance from the system?
[Nick Fury] I know you erased my password. Probably deleted my retinal scan. But if you want to stay ahead of me, Mr. Secretary, you need to keep both eyes open.
What did Fury mean by both eyes open? A simple mention that he doesn't trust anyone, so you have to pay attention to your friends and enemies, or is there something deeper?
If SHIELD deleted Nick Fury from the database why would his blind eye still have security clearance?