The great thing about software is that it can be recreated, reghosted, reimaged, redeveloped, and upgraded. While Smith was primarily destroyed by Neo, eventually freed from the system, and finally obliterated (like a Trojan being wiped by AVG). But unlike humans, machines do not forget to “back-up”. Somewhere, contained by the confines of the world of the machines, is another version of Smith (perhaps improved), ready to be deployed as a weapon at any given moment. The Trukstop.com