Which part, that Khan and Chekov recognized each other in
TWOK, or that Khan met Chekov while strolling down the corridor in
Space Seed? It is most probable that Khan and Chekov did meet on the Enterprise during
Space Seed; we don't know the exact details. (Option 1)
Going back to my previous analysis on the 2283 date and 15 years ago, it puts Kirk's and Khan's last meeting no earlier than 2268. If you assume the 300 years between air date and in-universe date, then Space Seed occurred in (Feb.) 2267. Did Kirk (with Chekov now on the show in Season 2) revisit Khan about a year later in 2268? (Option 2)
I got the "feeling" that Kirk/Spock had no intention on ever revisiting Khan based on their closing dialog (back to Option 1):
SPOCK: It would be interesting, Captain, to return to that world in a hundred years and to learn what crop has sprung from the seed you planted today.
KIRK: Yes, Mister Spock, it would indeed.