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I would export and import a lossless digital intermediate file,
and then do the time manipulations using that.
Yeah, I think I can turn my micro-sequences (every individual movement in its own clip) into mini-sequences (a series of movements in a chunk that doesn't need individual adjustments). Export and reimport and then I'll have the flexibility to alter individual pieces so that they sync up properly, but not have to change each tiny clip separately. Sounds reasonable. Does anyone know why I'm getting these extra frames doing it the way I am though?
It's because what you are doing is changing the speed
of each individual clip, not the sequence as a whole.
But when I go in and change each one individually (click to select, right click, speed / duration, enter new speed, ripple edit on) it keeps only the frames I kept when I edited. When I select all clips and change speed (select all clips, right click, speed / dur, enter new speed, ripple edit on) I end up with frames that I had previously edited out showing up.