We don't know how old the Turtles were before the mutagen bomb went off. Most likely the Turtles, Karai and the Foot, etc. all existed as we know them for 2-3 decades before this happened.
Remember this is 50 years in the future. I seriously doubt it happened immediately after we left off. You really think Raph and the others didn't see Leo for 50 years?
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