@Andriy Knysh (Cloud Posse) this one warrants a closer look and is an area you've spent the most time on over the years.
github.com/cloudposse/atmos/pull/2787
I don't know when it stopped working, but this formalizes and adds regression tests to ensure a "parent stack" can be decomposed into smaller files. It preserves the idea that component instances are unique, while allowing them to be split across multiple files.