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@raafal - I'm pretty sure the spanned archive (part-0001.calibre-data etc) can be unpacked using the calibre-debug command, but it doesn't seem to be documented - something like '--unpack-calibre-data' I imagine. Hopefully someone will chime in with the right answer.
If you have the library and configuration directories on the 32bit linux system you could probably just copy them to your 64bit linux system - file systems permitting of course.
BR
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