The config is all stored in XML text files so if you want to exclude certain parts of it you can copy/zip-up the files except the ones you don't want. (Or preserve the files you want unchanged, restore a backup, then put back those files over the top.)
/dopusdata\ConfigFiles\favorites.ofv is where the favorites are stored.
More info here: [HOW TO: Backup or locate your Opus configuration (Advanced))