Moving this to InDesign forum, since it doesn't relate to CreatePDF service.
@Chábæna – there are several ways of doing this:
1. Create a new book from the File menu => New => Book
2. Load all your InDesign files into the new book, save the book
3. Export the whole book to PDF
1. Export all chapters as single PDFs
2. Combine all the single PDFs with Acrobat Pro
*If you are using InDesign CS5.5 there is a bug that could lead to false page numbering of your auto page numbers
So go the way I recommend in route B.
Read about book creation, the book panel and its features at:
I'm guessing you have an InDesign Book (.indb) file and you want to export the whole thing to PDF. To export the entire book you must have either ALL of the component documents selected, or None of them, in the Book Panel, then the Export Book to PDF command will be available. If you have only some documnents selected in the panel you will see Export Selected Document(s) to PDF.
And Export Book to PDF is in the flyout menu of the Book panel.