I assume you are talking about calibre settings? Sorry, but I find the notion of a calibre 'factory' amusing.
In any event, you can erase the saved conversion settings for books by selecting the books in question, opening 'edit metadata in bulk' (the E key if more than one book is selected), choosing 'remove stored conversion settings for selected books', and pressing OK.
For the preferences, use the 'Restore defaults' button available on every dialog.
If you *truly want* to reset completely to default, then:
1: start calibre. Go to preferences -> advanced -> Miscellaneous.
2: choose 'open calibre configuration directory'. A file explorer should appear.
3: quit calibre.
4: delete all the files showing in the file explorer. The files will have names like gui.py, gui.json, global.py, iterator.pickle, save_to_disk.py, and many more.
5: start calibre. You will be started in the welcome wizard. Tell it where your library is.
I suggest that you make a backup of the configuration folder, just in case you find you don't really like starting over.