Yes, they made an ending for the Decade rerun that cuts the elements introduced in the last few minutes of the series that ended up irrelevant to the final version of Movie Wars (like Yuusuke getting brainwashed and Diend shooting Decade) and replaces those scenes with... something else.
I wish everyone who got into Decade and watched it these days watched those new versions rather than the original one. At least, the first time through the series. It's not even a matter of opinions about the ending, liking one more than the other, it's just to avoid making people watch a lead in and preview to a movie that doesn't exist. The original ending is only relevant if you're actually interested in the production side of the things.
Movie Wars has problems of its own (and... some weird creative decisions), but the lack of direct continuity with the original cliff hanger really doesn't help people's opinions about it and the Decade series in general.