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Well, obviously things that refer to specific locations on your computer have to be stored as paths. The path to the currently opened library being one of them.
You can work around that by creating a shortcut to launch calibre that uses the --with-library option, then it wont used the stored path.
And note that I recommended syncing iterator.pickle not the entire config directory. Although, syncing the entire config directory is perfectly possible, I do it myself.
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