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One very easy way to do it could be to automatically run a program when you exit calibre. Launch calibre from a script. The program then updates the alternative folder tree with new/updated links. I do something similar to sync a backup copy of my calibre library using rsync. Takes seconds usually.
There could also be a separate "resource" folder tree with files that calibre is not suited to manage. If names of folders/files match metadata in calibre these resource folders/files are also linked in the alternative folder tree.
By linking less space is used and no data has to be copied, so it should be much faster than an actual sync.
To make sure the calibre library is not corrupted the linked files would have to be read only.
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