As somebody who has taken notes for a long time now, I have gone through iterations of my setup to interact with them (last year I tried to use Agenda for my periodic and project notes, which I later abandoned in favor of using exclusively Obsidian again). In the process of moving from one app to the next it was not uncommon to leave notes behind. Not always did this happen intentionally. My current incarnation of my notes system consists of about 5000 notes, when I started to move from Evernote to Obsidian I left thousands of notes behind. If I’d need to guess, a count of all of my notes ever written reaches probably around 100000. As I have a full-time job, a little family and little time, my current situation doesn’t allow me to do work on my notes all the time.
So I will probably never be able to collate, deduplicate and unify all my notes into my current system. But I have learned that this is really also not as important as one might think at first. I use my notes system as a way to think and generate new ideas. The argument for having a notes system like this continues usually this way: “…and the more ideas you have, the more you’ll create/find…”. But I think more important than the total amount is to reach a critical mass of notes, which seems to start for me around 50 or so. By this point I seem to be able to always find something to connect to something else. There is always something else to elaborate, so ideas are generated, which is exactly the goal of my system.
I don’t need all my 100000 notes to do it. These 50 notes also don’t need to be perfect notes, or only capturing “atomic” ideas. Some are short reflexions, others are definitions, quotes, maybe a picture, a copy and pasted line of code. Often times they are daily notes that log what I have done that day with links to other notes. (See also: The three types of notes I take)
Heterogeneity and being in various states of completion are really not a problem, as long as there is enough of a critical mass in the system to generate new notes.
EDIT: You may be interested in my little constellation of “Notes on Notes” about the process of working with a notes system: