After posting what is below, I realized I was responding to you , who I have seen on here probably knows all this. Oh well. Maybe it will help someone else.
What breaks links is when you rename the files in your vault while outside Obsidian. When you rename something that is linked to while in Obsidian, you should see a little message flash in the top right area of the interface telling you “X links updated in Y files”.
But this won’t happen if you rename it externally. The files will still be in the vault, but all links to it will tell you that note hasn’t been created yet, if you ctrl hover over it. Of course, if you ever do this, I would imagine that by just renaming the correct file to its original name, the old links should work again, but I am not 100% sure, so don’t quote me on that.
But yea, rearranging notes within new folders within your vault while outside of Obsidian should be just fine. I have never had a problem. The only other problem causing issues I have had were placing two identically named files in my vault and having notes that exceed the max path length allowed by operating system even if you have max path setting disabled in registry in Windows.
Hope this reassures you. I know I had trouble believing that Obsidian would recognize markdown files I didn’t create natively at first, but it does. You just have to avoid those few gotchas I mentioned. Hopefully I didn’t forget anything.
I didn’t think it was possible to select multiple files in Obsidian explorer.
Good luck.
