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It seemed that it was suppose to be in canon with the original trilogy. I believe I remembered that someone in the animation that Splinter was suppose to even be missing a piece of his ear.
You can take it either way, kind of how like Next Mutation (outside of Shredder) seemed to be kind of a continuation. I mean wasn't the lair suppose to be set up the same as the lair in the live action movies?
Personally I do consider it as part of the continuation. Doesn't hurt any of the films if you do count it
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