[itimpi]

Note that Calibre does NOT know the location of the original eBook. When you add a book, Calibre makes a copy into it's own folder structure leaving the original unchanged.

If you want to update a format in the Calibre library then probably the easiest way is to open the Edit Metadata dialog for the book in question, and having done that drag the new book to the formats area of that dialog. If the format does not exist, then it is added as an additional format. If it does exist then the new one replaces the old one.

It sounds as if what you have been doing is creating additional book entries in the Calibre library. It is perfectly permissible in Calibre to have multiple entries for the same book if that is what you want. However then each entry has it's own copy of the underlying ebook files. I do not think that is what you are trying to achieve?