everything up to "The strange thing is that I had this working...." is expected.
what do you see when click control>test movie>in animate?
Indeed, I thought Animate had removed the ability to embed video files in SWFs. Or maybe it only works with FLVs? It's not something I've personally experimented with.
you can load an mp4 into a flv_playback component with no skin (like the op described) and export the video ok.
If the overall goal is to have animation and sound that goes on top of an existing video track, this would be the best approach:
1. Keep your high quality video file. Make another one that is H.264, it can be any quality or data rate, you're not going to use it in the final video.
2. In Animate, File/Import/Import Video/. Choose the Embed H.264 video option, and import that H.264 file you made.
3. Do all of your animation, by scrubbing the timeline to get the timing right. For sound, use the uncompress WAVs that you have (but make sure they are 16 bit 44.1 kHz), and set their sync to Stream, so that as you scrub the timeline the video will stay in sync.
4. In Publish Settings make the sound settings be Raw, 16 bit, 44.1 kHz.
5. File/Export/Export/Export Video. Check the box that says Ignore stage color (generate alpha).
At that point you'll have a large MOV file that has an alpha channel. Import that into Premiere, and place it on top of your original high quality video. Then export the project to get your final video file.
Thank you. I'll have a look at that today. Currently, although the timeline shows the placed MP4 as just populating the first frame, on testing the movie in a browser, the whole thing does play. However, this makes animating around it absolutely impossible, so I shall try this method out and see how it goes.
Colin - thank you! Learning more and more as time goes on. Perfect!
In the long term, it would probably be best to learn After Effects for this sort of thing, as Animate clearly isn't intended for it.