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@Geremia - The real question is why did you lose them - that shouldn't happen when you upgrade? I've gone though 100+ upgrades on Windows & Linux in the ~3years I've been using calibre - never lost a single thing.
I think VL's and Saved Searches are in the metadata.db file. They are 'backed up' in the metadata_db_prefs_backup.json file in the library. Are those files present in the library folder?
Suggest you do a file system backup of your library folder as it is now - ie copy it - lock, stock and barrel - to another location.
You could then run Library Maintenance->Restore Database, that will rebuild the metadata.db from the metadata.opf files in the book folders AND the metadata_db_prefs_backup.json file.
BR
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