I just realize it could be much easier. All you need is the mid bottom part(s) (as in my example) where the water drips out and 1 background.
So with an image editing program like Affinity I would crop the part out that contains the moving parts.
To do so, I would load all images into separate layers, define the cropping area, crop so all you have left is the parts that have movement then save each frame. Go into Hype, load one un-cropped image as background then load the cropped images above the background into a new timeline and position them so they line up with the background.