In Markdown Navigator links are created to files and find usages generates references to files.
If a single Java file is moved then no file references to the Java file will be updated causing broken links.
However, if the Java Class file is moved as part of several files then file references are updated.
This seems inconsistent and probably is an omission since a Java Class move involves a file move and should update references to the file, not just the class.
Is there something I am missing or should I open a YouTrack issue?