1. Yes, that's the purpose of testing your dev app. Make the changes to the InDesign source files, use the Folio Builder panel to update your articles, and then use the Folio Producer on the web to update your published folio. Then export a new .zip file. In the Viewer Builder, select the viewer you created and click Edit. Specify the new .zip file, follow the prompts and download and test the development app.
2. Yes, revoke the current certificates on the Apple site, create new certificates using the Apple computer, and specify the new certificates when you re-build your viewer. If something goes wrong with your serial number for any reason, you can always contact Adobe to have the issue resolved. You should not pay twice for the same app. Just let us know if there's a problem.