It is not the PPC's modus operandi to allow a young Sue to run around in the multiverse unsupervised just because their parent sent them away. They find the Sue-babies, make sure that the children do not pose a threat, and then bring them back to the Nursery, where they will be properly educated in the ways of canon and in being non-terrible people by the Nursery staff and the Nursery Flower, Professor Beans. Several stories have detailed Agents bringing back badfic babies, whether they're Sue offspring, slash pregnancies, or otherwise impossible births, so it's not hard to conceive that an Agent's backstory could deal with them being a former Sue-child. Maybe a misplaced adjective caused rapid aging, or the child has simply been in the Nursery since the first Pokémon badfics back in the 1990s, or something of the sort.
If you're wondering how the Agents would be able to find the baby if the Sue teleports him or her away, that's actually been addressed in a few missions in a few ways. Essentially, due to the way the Word Worlds work, a vagueness of surroundings can be altered slightly by Agents with strong enough willpower, as long as they fit the canon involved and do not contradict any of the Words. A command as vague as "somewhere else" could easily be shaped into "not here, but over there, behind that tree". If the field Agents couldn't do it, the DIA would probably be sent in for cleanup, and they would be able to shape the undefined command enough to find the baby.
Secondly, I'm not sure what you're getting at with a "reformed author". Would the original author know that their Sue was killed, and create a sequel series around the baby? Because they tend not to. Also, if the author was reformed from creating Suvians, they probably would not have written a heterochromic cat-hybrid in the Pokémon continuum unless they were doing it as a joke.
In addition, just because a character is a secondary or a supporting character, this does not make them non-Suvian. In fact, it can sometimes make their Suvian characteristics harder to detect, since the Sue wouldn't have as much screen time to display them, and thus make the character more resistant to reformation.
And I really didn't understand the last section at all. The former Sue-baby is used as a main character in a new fic because the original author was jesting with a younger sibling, and this somehow leads to the PPC finding and recruiting them? Agents usually tend to kill any bit characters that are abnormal enough to be unable to assimilate with canon, for one, and again, this one is a heterochromic cat-hybrid in the Pokémon continuum, so it's practically impossible to assimilate. Sometimes the Agents will recruit bits, if they're interesting, entertaining, or surprisingly well-rounded, but they wouldn't likely recruit a character showing above-standard levels of Suvian traits. Also, I'm not sure how the last section ties into any of the rest, since linking a badfic bit character with the complicated PPC-related backstory just seems to be unnecessary and a bit contrived. It seems like there are two ideas here, one a former Sue-child who now acts as an Agent and one a character passed off to a badfic writer who wrote them into a poor story that attracted the PPC's attention, and they don't really mesh.