In the olden days I would often do stuff like this with flash.
Looking at the animation made by hand drawn I would use the end frame still to start with and make it a static background plate across all frames.
I would then add shapes to hide what should not be seen in the first frame - those shapes would be the same as the background colour. The next frame is then the first frame less some of the shapes that obscure the background plate, the third frame has more shapes removed.
On frames where the lines are and they change position, I would take that section from the image and just add that cropped line over the base image as required.
I might have done this via masking in flash.
Trying a flipbook effect of the whole frame is going to be a nightmare because any misalignment will cause jitters. Taking a single frame as a backdrop and changing what is seen
via an overlaid shape will keep everything rock steady.
This really is a simple job.
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