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Using the same calibre library alternating under Windows and Linux will lead to trouble. Most likely that is what you have discovered. Even using calibre on a networked filesystem may lead to trouble, and is actively discouraged by the developer. Don't risk it without a good backup system and heavy testing.
Cut your losses and try to salvage what you can from the library as soon as possible.
That said, I have my calibre library on a Synology NAS, and mount using NFS from my Ubuntu desktop, and it works fine. But I don't use it from any other computer or operating system.
Check under related tools. I belive some here use the webbserver on their Synology NAS to share their calibre library using different tools, like COPS or Calibre2opds.
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