[BLOCKING Christmas Content] Strange Inconsistent Cloning Behavior

Verification builds: 1.2.5 (all builds and release)
Summary: (this worked perfectly in 1.2.3 but broke in 1.2.5)
Can be best explained in this video but I will retype here: https://youtu.be/arJuWSeM3TE
Essentially, we are cloning in frames from a template structure in a very far away tickingarea. We do this many times in the map but it only affects this one instance. Despite there being no problems with the template itself, every time you run the clone command, a different random chunk of the structure is missing. You can see it in action in the video.
I don't think it's just a visual glitch though because you can walk into the hole (normally if there's a visual lag you just stand on invisible blocks). The blocks reappear in the next clone command.
Impact: The player could be suffocated by falling in to the hole and also ruins the effect of the event.
Repro Steps: I'm not sure how else to reproduce it.
Observed Results: Inconsistent chunks of cloned area missing.
Expected Results: Consistent clones
Screenshots/Videos attached: Yes