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The project would be easier if you used more layers. It looks to me like you are trying to do too many things on a single layer.
If the camera is locked I would export a frame to a PSD and then remove the background in Photoshop. Then drop this layer behind the rotoscope owl head.
If the camera is moving or there are other things that are moving in the frame I would duplicate the layer, maybe even Stabilize Motion so the branches are not moving, then use the clone tools to completely remove the owl's head. And then put that pre-comp below the rotoscoped head.
Some more workflow and shot details would really help us point you to a more efficient solution.
One other proint. The clone tool is kind of difficult to use and requires quite a bit of study to use properly. I would suggest that you spend some time with the help files or community resources by typing Clone tool in the search help field at the top right corner of AE. You'll find some very useful information.
Thank you, Rick.
After a few of hours, being away from my project, I realized that I simply needed to pre-render those 2 good layers (normal and time-inversed), then import the new video file into the project and duplicate it as many times as I want.
But yes, I will study the Clone Stamp Tool a lot more, it really works in a mysterious way.