If see the message "File can not be normalized and will be included as a linked document" when hovering over an upload PDF file, or if the 'Page Count' for the uploaded PDF file is 'unknown' after uploading a PDF document, this message indicates that the uploaded PDF file is a non-standard PDF file that can NOT be merged with or combined with your generated application. Instead of combining it with your Generated Application PDF file, this uploaded file will be referenced in the Generated Application PDF as a link to the actual non-standard PDF file you uploaded.
This situation is ok. however, if you are able to convert the file to a standard PDF format, that would be preferred. See the FAQ on help with Adobe PDF files for more information on converting the PDF file.