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When fixing metadata within Calibre the underlying folders and files get automagically renamed.
When you use Save to Disk feature you are actually "exporting" the books and metadata to a folder without any control or sync with Calibre database (metadata.db).
Therefore, what you have now is duplicated files and folders, without any reference from within Calibre. This and other reasons took me to open a ticket for Integrity Check feature request.
To recover from your current situation, I would recommend you:
- Move folders that do not end with "(number)" out of Calibre library folder.
- Use a specialiced tool to look for duplicates between your moved files and files in Calibre library, deleting those out of Calibre.
- If what you want is only LRFs, just go and delete LIT files.
- If you want to keep both, just add LIT files as additional format available to each book (not sure how to automate that, though).
HTH.
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