There isn't a way to combine H.264 with animation. You don't have to recreate everything in Premiere, just export video from Animate and place that video in a layer on top of your existing video.
The H.264 that you use in Animate can be low quality, you're only using it for timing. Then in Premiere you can be using your high quality original video, which need not be H.264. When you have the animation on top of that video you can then export the two combined into one H.264.
I know that it would be nice to export straight from Animate, but then you would be recompressing the H.264, which wouldn't be as good quality as going straight from your original high quality video. Also, Animate doesn't export H.264 anyway, so it would require QuickTime and would export a very large MOV file, which you would have to send through Adobe media Encoder anyway, just like you would when going from Premiere.
Thank you Colin. I know quality is an issue. But the two step exporting makes it very cumbersome.
What puzzles me is that FLV is discontinued without a replacement that has the same functionality.
(I just tested that method again, and the deal breaker isn't even the exporting, but the fact that I can't even preview the animation (Command-return), so I can't see how Movie Clips behave in relation to the video, unless I properly export the whole project).
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Quality wise you wouldn't have wanted to do that with FLV, unless it was for perhaps a web activity where the quality didn't have to be the very best.
If you subscribe to Creative Cloud you can install older versions of apps, like Flash Pro CS6 for example. That includes Adobe Media Encoder CS6 (which does not appear in the old version list for AME itself). That's what I do, and then use AME CS6 for making FLVs.