Paulo,
Copying and pasting the root folder should work as long as the assets maintain the same relative folder path as the project file, either in the same folder or subfolder of the project path as they were before.
When you export a package, it will only grab the files that are currently linked to items in your project (models used in your object manager, images and videos selected in project materials, fonts being used by scene fonts, etc.) which is why your finding certain files are not showing up when you deploy to a new location. The "Maintain folder structure" checkbox replaced the "include unused files in project folder" checkbox in Version 11. It helps to keep subfolder paths that Dynamic Materials and scripting may rely on, but no longer includes files that aren't currently used by your project.
On occasion, I've found a combination of the two methods to work...package your project to maintain the links for image and video paths to materials., etc., but also ZIP up or copy the root folder of the project to the deployed location of your project package so the rest of your assets become available on the new machine.
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Jeff Mayer
Ross Video
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