Most likely it was a combination of many things. Janet Hubert-Whitten got pregnant while they were making episodes for season three. The producers got around this by having Vivian Banks be pregnant. Late in season three Vivian had the baby, but in real like, Janet Hubert-Whitten was still pregnant. Once Janet had her baby in real life, she had to take care of him (or her, I don't know what she had), so she couldn't dedicate that much time to her work until the baby was mature enough for having someone other than his/her mother to take care of him/her.
There are other versions that tell that when Janet Hubert-Whitten was pregnant, she became difficult to work with. She allegedly had problems with the producers of the show, and some people said that Janet blamed Will for turning the producers against her, which eventually got her fired.
Who knows if we'll ever get to know the real truth.
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