I did not read your post very carefully, but apparently you already did indeed the same as I did.
With a default Copy & Paste, KiCad clears the annotation, which is sensible, as multiple parts with the same annotation leads to *&^%$#@!.
However, if you press the right mouse button, there is a Paste Special in the popup menu (Also accessible via the main menu: Schematic Editor / Edit / Paste Special) With Paste Special, you have an option to preserve the annotation.
In your diff, the UUID’s and the coordinates change.
In KiCad the UUID’s always change. They have to, because they have to be unique, that is what one of those first two U’s stand for.
The coordinates could be kept the same relatively easy, for example by placing a dummy resistor at (0, 0).
So I combined this and chose: Keep existing reference designators, even if they are duplicated in the Paste Special operation.
The result is visually nearly the same (I kept the reference resistor at (0, 0)).
Beep_2022-03-28.kicad_sch.zip (21.8 KB)
All the UUID’s have (of course) still changed, and stuff is in a different order in the file and this confuses diff programs.
Also, KiCad uses the UUID’s by default to match schematic symbols with PCB footprints. To fix these (now broken) links, you can simply do: Schematic Editor / Tools / Update PCB from Schematic and then select: Options: Re-link footprints to schematic symbols based on their reference designators
