Whilst looking for a solution to the problem I encounter in my blog post about run cycles, I found an Autodesk help document about time configuration. The document goes through the progress of shortening an animation, and notes that sub-frame animation should be used. Instead of being based on frames, sub-frame animation works by positioning frames as timestamps instead. Instead of setting a frame on frame 42, for example, it would be set at 00:03 in.
Using this is apparently better for re-scaling animations as you don't lose frames in the process. I tried turning it on and adjusting my animation to get rid of the jutters, but even after my efforts, the problem was still arising. I also read a document on frame snapping and tried to adjust the timeline to make it more seamless, as you can see below. Although I think this helped slightly, I can still notice the animation juttering as it loops.
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