This was frustrating me, too, and I knew about the index note idea, but it seemed like yet another separate thing to update (and which could easily fall out of sync with my actual files), so I never really did it.
I did the thing you’re not supposed to do, which is to treat my folders in Dropbox like the index. My Obsidian vault now wraps around my whole JD system (which actually works better than I thought it would, with many folders excluded from syncing). In Zotero, there are some things replicated (folders related to academic publications or classes I’m teaching), and they get the relevant number prepended, mostly so I keep seeing them and remember what the numbers are (which I still don’t really). In Things, I replicate the top-level areas from JD as areas of responsibility, and some projects end up with JD IDs on them (this is the loosest part of the system now, but I’ve been using Things forever, so it’s been a slow process integrating JD in there).
Not a solution for your problem at all since I really have tried to keep only one note system and one file system, but I figured it was worth having here on the thread. (At the very least, it seems like your file storage may correspond to different areas in your JD system? So you could know that 30 lives in OneDrive, etc., and avoid conflicts that way. It sort of depends what your reasons are for maintaining separate notes/files; if those end up corresponding to areas, then you wouldn’t have much issue with conflicts. If you find a lot of crossover at various levels, that might also be a sign that there’s a more organic way to sort your system so that the tools you use do deal with mutually exclusive areas?)