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Your workflow is faulty. You have two options. The first option, Perfect the edit Duplicate the sequence to keep things easier, then, using the duplicate sequence using Dynamic Link, open one clip at a time in After Effects, run warp stabilizer on only the frames you need to motion stabilize, render a Digital Intermediate using a suitable Mezzanine format (visually lossless frame based codec), then replace the footage in the original sequence. Do Not try and dynamically link multiple shots at once.
Your second option, Render your Premiere Pro sequence to a suitable DI format, import the footage into After Effects, Create a comp from the entire sequence then split the layers on every cut and run warp stabilizer on the layers that need it.
Thank you for you response Rick! I will use the second option.Going forward...what would be the appropriate work workflow when using a multicam sequence to adjust selected clips in Ae with the track motion stabilizer (I don't like the result of warp stabilization in Pr).
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Track Motion Stabilizer is entirely different than Warp Stabilize. I didn't enlarge your screenshots to see that you are doing Motion Stabilize with at least position scale and rotation. You should not add scale to the motion stabilize because the background is close to the subject and parallax shifts when you also stabilize scale the shot can make the background look very odd. Also, looking more closely at your screenshots I see that you have tracking data from one shot but have applied the stabilization to the shot above. This means that the target was the second layer. Renaming layers and paying attention to the Target dialogue in Motion Tracker will help keep things straight.
There is also nothing preventing you from putting the CTI at the first keyframe in the top shot, selecting Anchor point keyframes and cutting them, then paste them to the second shot, then doing the same with the rotation. You can just delete the scale keyframes. If you are getting stabilization applied to both shots at the same time then something else is going on. Maybe renaming the layers ould help.That's what I get for answering forum questions on my phone.
You should always pre-edit raw footage somehow so you are not wasting time processing frames that are not going to be in the final cut. It's OK to change your mind on a cut after processing footage in AE but it's horribly inefficient to process footage that will not ever make the first cut.
If I a using Dynamic link I always just select one clip or all the clips in a stack, I never dynamically link a sequence of shots. If I am going to open a Premiere Pro sequence in AE I will always duplicate the sequence and trim it to include only the shots that should be in one composition. I never create an AE comp that is longer than a single thought, phrase, or sentence. You will not find any five-minute comps in my AE projects. Most are a single shot under seven seconds because I mostly work on dramatic films and most cuts are under 7 seconds.
I hope this helps.
You have been very helpful Rick, thank you!