The LOOP.

Meta> Smith knows about the first perfect Matrix. He says as much in M1, when he interrogates Morpheus. No one knows if he’s aware that the Matrix has looped six times.

However: There’s reason to believe that he (Smith) does know. Why else has his programming started to malfunction. He tells Morpheus in M1 that he (Smith) wants OUT. “It’s the smell.”

There IS no reason to think that deleting the original Smith would delete the clones. A virus isn’t removed, just by deleting the original virus once it’s spread. What Neo/Deus used to delete the entire Smith-virus was the CONNECTION between the Smiths. That they had the same program source-code.

probably, smith knew bcoz he was told by the "system"

Or by taking over someone who knew.

its kinda like copy/paste. smith copied himself over everyone, n then to delete him was kinda like, neo did search on "smith" came up w/the results "smith, smith (2), smith (3)..." n hit the delete key

I'm pretty sure the machines deleted Smith, not Neo.

yeah, wasnt that what happened when they shot the 'anti-virus' thing thru him.

they needed neo to make the connection (hence smiths hand in neo)