I *highly* recommend using After Effects instead of photoshop for this kind of work.

Basically, you'll save the step of exporting the frames, modifying, then reinserting them. Instead, you paint a "traveling matte" that you modify as needed, with the possibility that you don't have to draw a new one for every frame.

This is how old-school effects shots are modified (wire removal, etc) these days, and I did a little training for it at Technicolor about 8 years ago. I'm sort of handy at it, or could get back to proficiency very quickly.

If you would like to share the offending sections of footage with me, I'll get to work.