I found these 2 method via Google, in this thread titled: Re: Flattening PDF Files at the UNIX Command Line.
_Method #1 - using Imagemagick's convert:_
$ convert -density 300 orig.pdf flattened.pdf
**NOTE:** The quality is reported to be so so with this approach.
_Method #2 - Using pdf2ps -> ps2pdf:_
$ pdf2ps orig.pdf - | ps2pdf - flattened.pdf
**NOTE:** This method is reported to retain the image quality.