I did some preliminary research on this and it seems as if it might be possible but it's beyond my current skills.
Alterations would be done to some PNG frames in one program for example and then those PNGs would be
mapped to the frames in the compressed video frame by frame or pixel by pixel.
It involves timestamps, keyframes and all that jazz. This would profoundly mean that the limitations of compressed
videos would be possibly removed. This may be too good to be true. It may not be possible due to the nature of
compressed videos, I don't know. Be cool if it was possible. Back to the drawing board.