Hi, I would consider to have all the files on the USB, have an autorun to start your html that wraps your main swf. Each link point to resources (other .html) located in folders on the USB and other links to online pages (http://company.com/pages.html) to ensure the stability. You need to be careful how you treat your links, depending on how a computer maps the drive, the link might not work. When exporting the files, location references are created so if you copy-paste the files somewhere else, the links are broken, resources are not found and web pages are blank. You need to export to the USB instead of copying files across so the links include the USB location.
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