[Jack Greasley]

One general answer is to break the shot up into several shorter sequences and stabilize each of them separately.

This will work generally for any techniques involving motion. (i.e. motion tracking, image stabilization, travelling mattes, automated roto etc etc.)

The solution already given is an AE specific version of this.

I recently used this technique to motion track an object that left the frame and returned. Rather than try and do it in one track, I just cut the scene during the time the object was not present and set up a new track for when it returned. The final appearance is a continuous track

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