I had animated some hundred frames before I realized there was a dot on the sensor. Is there an easy way to remove it?
Apparently, Dragonframe saves two versions of every picture, one with lower resolution and different settings, in which the dot is almost invisible. So the idea I have is to put the alternative images in a layer underneath the high-res-pictures and punch a hole where the dot it. A picture-in-picture.
Is that a good idea, or is there a better way?
You can also remove this dot from patch tool in photoshop, It wouldn't flicker and my suggestion is to use Hi-res file that will be you original qualit, low res file only helps us to view the animation.
I think your option for fixing this would work very well indeed. You would have to stretch the lower resolution version up to the size of the high resolution version, and I would suggest making the eraser a lightly feathered one, only ever so slightly larger than the spot.
Another option you could do is use the Clone Stamp tool in Photoshop. Again, set the brush to a small, lightly feathered setting, and select a colour next to the dot to replace the dot with. It's a very powerful tool when used well.
Last option, is obviously to reshoot.
Another suggestion I would make in future is, whenever you are shooting a new shot, shoot a clean frame of the scene, with no puppets in it as a tool you can use to clean things up afterwards. This wouldn't necessarily help in this case, but there are many situations (including rig removal) where it's very useful indeed. I normally remove the puppets at the end of the shot, and shoot a clean frame then.