Colon's "win" was never recognized by the NWA. The match was in Puerto Rico, during a house show, just to give the Puerto Rican fans something to talk about. It was never a legit title win, just like the Rockers were never officially WWF Tag Team champions.
Actually, it was to establish Capitol Wrestling's title. Back then, there wasn't a television deal like it is now with WWC and IWA in the island. Colón (notice the accent there in the second o) had established the promotion but wanted to give credibility to it, so he brought in Flair and had a match with him. The whole event was basically a plan to get the Main title in Capitol some prestige. Back then, there was nothing better than beating the man, who was the NWA champion. Since Flair was the man, it would have happened and Colón would the champion, which generates some prestige to the Heavyweight Championship in Capital. TO this day, the title's still around the island as the WWC Universal Heavyweight Championship since that's what the feud was about (our bookers have shitty storylines but the match layouts are slick Don't ask me why).
Kayfabe wise, this translates as Colón beating Flair, who's known as the Dirtiest Player in the game. This can either make or break you, depending on what happened in the match. if, say, the titles were on the line in the Flair/Colón match, Flair would have pulled every trick in the book he knows. Since Colón beat him at the time, it means that he's pretty much similar to Cena, in a sense.
Cena vs. Colón would go the same route, but Cena would prevail after eating a Figure Four leglock (maybe from the turnbuckle post, since those happened every weekend in a Colón match), headbutts (Colón's headbutts used put over as "brutal"), elbow drops to the leg in order to work it and make sure Cena doesn't do an AA (this happened EVERY match Colón worked), Colón was from the era when a match in Puerto Rico would last 20 minutes, minimum (the televised shows would last like 3 hours or some shit like that. Still do, I bet)
Colón being homesick doesn't translate to anything when it comes to kayfabe since one doesn't go "Oh look, I'm homesick I miss my home omgz my son has a goatee" in the middle of the damn ring.
Cena would win this one after being taken to selling school, taught by Carlos Colón and his crazy cartwheels (this was the equivalent of hulking up; it made the crowd go batshit crazy)