Palladium Books formally announced the loss of the licensing rights to Teenage Mutant Ninja Turtles in issue 9 of The Rifter and had to sell off or destroy their entire stock of Ninja Turtles book by the end of that year. Nine years later, Teenage Mutant Ninja Turtle "canon" was solidified by the TV Movie Turtles Forever, which establishes that the universe of the gritty black-and-white original comics (which is part of, or at least very close to, the Palladium Megaverse as it existed through 1999) is "Turtle Prime," a sort of hub from which extends an entire Turtle-verse,** containing ALL iterations of TMNT.
Back in 2000, Palladium published the first major update (as opposed to expansion) of RIFTS earth, the Seige on Tolkeen series, changing the aesthetics and landscape detailed in the original core book considerably. In 2005, they published RIFTS Ulitmate Edition, and eventually republished the early RIFTS books to expunge any mention of TMNT.
So is Turtle Prime still connected to the Megaverse? Most of the RIFTS books that mentioned TMNT have been republished, but the one exception I know of is Mutants in Orbit, which details near outer space for both the After the Bomb universe (the canon future of Palladium TMNT aka Turtle Prime), and the RIFTS universe before Tolkeen's destruction.
** If this sounds familiar, it's because Marvel totally ripped off the idea for Into the Spiderverse. But that is perhaps fitting, as Spiderman-adjacent comics (Daredevil specifically) spawned the entire Marvel "Iron Age" that TMNT was developed for in the first place, and was rejected from as "too weird." Because they went out on their own, they developed and licensed their own original RPG to get added distribution in hobby stores. That, in turn, gave them the nerdy "street cred" that made TMNT seem edgy and cool to little kids, and that popularity turned TMNT into the entertainment juggernaut it remains to this day.