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Plugins will only work if all your configuration directories end up in *exactly* the same path as they were previously. So if you used a different user name, or a different variant of Windows for instance, this would not be the case and they won't work.
The reason for this when I last looked at this a while ago is that there was at least one calibre configuration file which stored full file paths to the plugins, hence why they need to be in exactly the same place.
So if for instance you moved from Vista to Win 7, or installed under a different user account then your paths to the plugins will be different requiring the plugins to be reinstalled. However the plugins themselves (or certainly the ones I have written) are self contained. You could then (after reinstalling plugins and closing calibre) copy the various .json files for a plugin (like "Goodreads Sync.json") into that plugins configuration folder, which would to keep whatever settings you had previously. That should work fine.
The only real problem scenario I can think of for some of the plugins is if for instance you end up creating a new library. This will give you a new library identifier, and as a number of the plugins like Reading List and Kindle Collections store library specific settings, then just copying across the .json files won't allow you to utilise those. If you were particularly keen and careful you could get in there and edit the .json files but it is a worst case scenario.
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