This is super interesting, when I opened it in a text editor I didn’t clock that text block. Good eye!
I also didn’t know to check the list in the Objects view to find that object, so this is an excellent learning day!
Due to @primal_healer 's sleuthing I’m upgrading to the most current version of Inkscape, and there’s even a bug fix in the Mac version titled “Stroke to Path : Converting an object’s stroke to a path no longer makes its clones vanish”
I’m not 100% that is a related/the problem, but it seems very in the ballpark, especially after your sleuthing.
Thanks so much! This has been bugging me for, no joke, YEARS. I am stoked on this thread no matter how this goes.