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Resources is for you Custom/alternate of standard items (these are your version of those found in the resources of THE INSTALL. The purpose of this loc is so Calibre Updates do not stomp on your customized...)
There is no single location. they need to go back where they were originally found
(user) Preferences go where they came from: usually the config folder or /Plugins (for those settings)
Alternate Icons go in /Resources/images unless the are part of a PI
custom templates go /resources/templates
If you did a backup of the original config folder, they should be in the proper paths
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