Originally Posted by Mick4545
Is there a way to prevent this?
No. That's how Calibre works. You have a source book, you Add it to Calibre, and Calibre puts it into Calibre's library. You can then delete your source book or keep it as a backup. Calibre works only with its copy of the book in its own library, and you should never need to go into the folders in that library. When you want a book, either "Save to Disk," "Send to Device" or just read it on your PC with the Calibre built-in viewer.