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For #1: if you use windows explorer to delete all the formats (a "format" is an ebook file) of a book from calibre's database (which you should not do but ...), you can delete the books from calibre's database by searching for books with no formats and then deleting the books.
In calibre:
1) search "formats:false". This will produce a list of books that have no formats associated with them.
2) delete any books on the list that you no longer want.
For #3: I am confused. I thought that you wanted to delete the books, but you are now talking about restoring them. To "restore" a format in this situation all you need to do is put back the file you deleted using windows explorer.
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