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Check whether youh have automerge turned on in preference adding books. If it is on calibre will merge duplicate titles.
calibre will import just about any file whether it handles it or not.
If you are using the first or second option under add books you can lose many if your files are not organised in the strictest manner.
Perhaps make a new library and use option 3 to add books and compare.
I used windows search and searched for all epub and added them via select all then drag and drop, then mobi etc.
Helen
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