Hi all,
I know this is a fairly old post, but I just came across it and wanted
to clarify things a bit. The "renamed referenced metadata defined
only in input map file" is used by our Incremental Obfuscation
feature. This allows you to obfuscate a class using a library that
was previously obfuscated but which you no longer have access to
reobfuscate (say when working on an update to a deployed application).
This setting tells Dotfuscator to apply the renames from the map file
to references found in the input assembly, without needing the
original assembly in which the type is defined.