1. Each time you export a version of your tour whitha new name create a new folder for it. That way you will not muddle up which files belong to which version of the tour.
2. If you've done that then you will need to upload all the files/sub-folders in that folder - EXCEPT the sub-folder with the source files if you have used the extended save feature top save the sources into that folder. Make a separate folder on the host server for each tour too to keep things tidy.
3. With so many pano scenes it would best not to embed the data nor the XML files otherwise the single SWF file will be huge and slow to download.
4. The fullscreen button/icon will only work if you load the tour via the HTML file, and you have chosen an HTML template that includes the fullscreen function. If you merely open the SWF file it won't work.
5. Consider switching to Panotour Pro if you already have an Autopano Giga licene and a krpano licence. Here's how to get a licence key for Panotour Pro:http://www.autopano.net/wiki-en/action/view/FAQ_-_Frequently_Asked_Questions#How_to_get_my_free_licence_of_Panotour.2FPanotour_Pro_.3F