No, this is pretty obviously a retcon; Splinter acted as surprised as anyone by the introduction of the Utroms and the dual revelations that Yoshi was a guardian and that the Shredder was an Utrom. While one can fanwank it, saying that this is just yet another thing Splinter kept close to his vest, it's still somewhat inconsistent with the way things were depicted in the first two seasons--fortunately, Splinter was already out of action during the decapitation scene in RtNY pt. 3, since the retcon really couldn't have worked otherwise.
All in all, a good cool-down episode. The turtle tots were much more adorable here than in their last appearance, and Splinter and the Ancient One were as father-like as we've ever seen them.
Random thoughts:
Wow: I love the level of detail in the Tribunal Monastery courtyard--that can't be easy to draw.
I've liked all of the Shredder's lesser mooks seen this season, and the one here is no exception--for a one-shot character, he's got a lot of personality. His voice was also spot on.
I also really liked The Ancient One in this episode, from his initial response to seeing Splinter, to his smile when the turtles go to bed, to the way he absolutely trounced the bone demon.
I'd really like to know how Splinter managed to retrieve both Yoshi's body and his sword (as seen in the Season 3 finale); ninja skills or no ninja skills, it sounds almost impossible. And I liked seeing Yoshi get a funeral of sorts here.