Or you use something like Obsidian, Logseq, Notion and so on that have already abstracted this problem away. You rename a file or move it to some subfolder and every single reference to it gets auto-updated without you having to do anything.

I'd argue that this sort of interlinking flexibility (alongside easy-to-use plugins) is what separates the current era of note-taking apps over alternatives that people seem to (ab)use: a folder of Markdown notes edited via VSCode, a Google Docs folder, or even a static site generator.

After wasting much time on fixing the bookeeping you'd get to the next basic issue - content search across devices. Then to tracking changes done by various people. Then... backtracking a couple of steps and dropping the whole thing