If I mark files with labels inside a folder and then rename the parent folder, I actually lose all the work I made to mark files with labels. (Because files are marked depending on their path and path in Preferences / Favorites and Recent / File and Folder Labels are not updated.)
I think DOpus should keep track of files and folders being moved (or renamed) so they are still labeled after moving.
It already works this way for collections.
The way it works right now is that labels apply to paths, not the actual files themselves. That's by design, although both methods have their pros & cons, and we might support the other method (or something similar) one day.
One way you could get labels that apply to files, not paths, is to apply comments or tags (instead of labels) to files and then set up label-filters which match those comments or tags. The comments/tags will then move with the files (provided Preferences / File Operations / Copy Attributes / Copy metadata and/or Preserve the descriptions of copied files is on, and the destination filesystem is able to store the metadata), and the filter itself won't point to any specific path.
(If something else overwrites a file then it could result in the comment/tag being lost, of course, depending on how it is stored and exactly how the other program edits/overwrites its files.)