Hi -- right-click your .xsf and select design. The form opens in design mode. To repack as an .xsn, you can use Save As from the File menu and save the template. At that point, the form you are working on will be the one located where you 'Saved As' to....
I'm guessing you saved your form as source files, then continued to do design work -- when we save as source files from IP, the template that remains open is now the version that is in the source files. Here's a link from Office Online with some more information.