You can click on all context menus (link mentioned, the 3 dot menu on any pane, and select “copy obsidian url” there.
I found that if you remove the path part of that file name, it finds the file for you anyways, no matter if it is in an odd place:
Original copied link:
obsidian://open?vault=Zettel&file=classes%2Fchem-1b%2Findex-chemistry.md
Works anywhere link:
obsidian://open?vault=Zettel&file=index-chemistry.md
Maybe the link that works anywhere could be made the default if it is not ambiguous?