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calibre truncates all paths in the library to less than 500 characters (relative to the top level folder) on non-windows operating system. That is well within linux file length limits. Though of course, as with everything on linux, there is no well defined file length limit, since it varies with filesystem, kernel and mount options. I'm guessing the OP is copying files to some unusual filesystem on linux, like a network share or a windows filesystem.
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