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It is my experience that after I run the jitter removal, I do not refit any frames. What I will do is adjust the frames by hand and then blend those frames together until they look very smooth and natural. When I say blend, I'm speaking of a technique that I'm using, not something that is really built in, but kinda. I've also mentioned it in other posts, recently.
Ok, so I've tracked all the frames I need in low res, and then gone frame by frame and refit poses. Maybe some minor refitting and manual adjustments are done, and the animation is ready to remove jitter. After jitter removal does it's magic, I go through the animation frame by frame again, looking for spots that jump at all or are not matching perfectly, and I adjust them all by hand. Then, to make sure it is all extremely smooth and fluid, I go thru those sections I've adjusted and turn smoothing up, usually only to 1 or 2. Then I copy the frame, and paste the frame and turn the smoothing back to 0. Then I goto the next frame and do the same thing, if needed. This technique gives you some better control over smoothing things out without ruining any previous work that was done.
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