When you promote yourself as a duo you will always been seen as duo. People don't understand what goes on behind the scenes.
That's why they stopped working together. When Kenan and Kel left Nickelodeon in 2000, they didn't want people to lump them in with each other anymore. They wanted to prove they could stand on their own. Or maybe Kenan did because I think Kel more or less wanted to keep working with him. Kenan was doing SNL in New York while Kel was living in Los Angeles, dealing with his own problems. They weren't in touch back then.
It was only in the last couple years that Kenan and Kel became close friends again. Kel said on TMZ back in 2014 that Kenan didn't want anything to do with him. I think Kenan eventually realized that him and Kel will always be seen as a duo, so he started embracing him again. But for a long time, those two were barely speaking to each other.