From what I recall, being alive when I was, she spent a vast majority of Season 31 (2000) studying zoology (she was often seen in the arbor with her large textbook)... I seem to recall one episode where Zoe was intrigued by this, and decided to write her own "Zoeology" textbook for her to study as well. I THINK it was also starting in this season, Gina was also frequently seen baby sitting her baby niece (or cousin) Hannah.
By mid Season 32 (2001), the garage of the carriage house was converted into a clinic for Gina's vetenary practice, with a "debut" episode of it, where she gives Big Bird and Elmo a tour of her new office and everything, while Elmo and Big Bird decide to bring in patients for her so she can begin working. It was also during this same season she would still frequently babysit Hannah... I remember a really sweet, yet toe-tapping little song Bob, Gordon and Maria sang to her about the different ways their guardians sang lullabies to them (it was here I learned that Bob was an Irish-American).
Afterwards, Gina slowly disappeared from the show to a similar extent as Susan - she was still seen on the show, but sparsley. Anytime we did see her, it was whenever a sick animal storyline... or like the time Elmo "fell in love" with Gina, and tried to worm his way into her office by dressing up as an exotic pet that needed medical attention from a vet.
Season 37 (2006) is when she adopted her Puerto Rican son Marco, which was a three-part story arc. I haven't been able to watch the show as much as I used to, so I really don't know how that plot device is panning out... I recall yet another Elmo story where he feels jealous because Gina spends so much time with Marco, so he starts acting like a baby to garner some attention from her as well. There's also been a few bits with Rosita and the two of them, as Gina made it clear that she would like Marco to be able to speak both English and Spanish (I believe Maria is also the godmother, as she went with Gina when Marco was adopted).
So, I'm guessing by Season 39 (2008), the producers decided that since Gina's a mother now that she needs to retire from her practice, because the carriage house was converted back into a garage apparently, only instead of being the kind of garage where you would park your car, it became a mechanic's shop.