Add Sencha Designer project folder to subversion (.svn folders with metainfo for Subversion are added). Open XDS with Sencha Designer and deploy project. See deploy directory: all ".svn" folders were copied as well as the project's metadata folder with content. Try to deploy one more time: deploy fails :-(
I have already migrated the project I work on to Sencha Designer, but because of that problem with Subversion I can't use it. It would be nice if you can fix that.