Shaun
Dear Shaun,
thank you for commenting! Relative links definitely break, if you reorganize your files. They are like web links that can break.
Foldie has a pro feature that allows to create file bookmarks and embed them in a virtual tree. These would be valid until you rename and edit a file. Also, file bookmarks have other shortcomings (more difficult to make them cross-platform).
If you look at files, it can really get philosophical: Is an edited file still the same file? Are the notes I have written about the contents of the file still valid?
In your case, you may want to create ad-hoc notes with links, that you throw away or rewrite, once you do your clean up.
Or you wait with linking until your files have settled. Or you change your working style in order to make use of links.
Use tools or conventions (like ForeverNotes) and you will gain benefits.
Thanks again for your kind review!
Joerg