wyBuild doesn't scan files with different filenames to see if they are similar to other files with different filenames in old versions. If we did that it would significantly slow down the patch creation process. That's why wyBuild only creates "delta patches" for files that have the same filenames in the new version as in the old version.
All other files are added as full files.
Why are you changing the filename for versions? I'll assume you do it so you (or your users) will know what version a particular file is. But why not just change an internal property of the file? For example, if the files are *.dll files you can just change the version property of the dll and keep the filename the same. Or if the file is some internal creation of your company you can add a special field to read the "internal" version of the file.