In some .PDF documents, it is possible they were created to convey certain
attributes of the original, in a way these can be related later to a recipient
over, say, an email/fax electronic document or other media; ColorSync can
be used to embed or enable characteristics otherwise lost.
That may include color, and quartz-based technologies in the original. And
there also may be encryption technologies specific to this document, too.
If this were the case, and the end product does not appear correctly, there
may be something else going on in that portable file document. While I
have no direct experience in these matters, I have found out about them
by accident and while looking into other details of a similar nature about
ColorSync and .PDFs...
• A brief technical note, TN2035: ColorSync on Mac OS X
...Does connect both ColorSync and the use of PDFs in Mac OS X.
There are other documents out there, some tell in detail and in short
path, on how to use these technologies together for specific purpose.
Other related information, such as encryption of PDFs via ColorSync
and diverse related topic matters, could be found by using Google to
search these topic words specifically: *Mac OS X colorsync in pdf*
While this may not answer your question directly, there may be more
to the situation than just having an incorrect app assigned to open a
document file; there may be more going on. The author of a custom
document should know what they did to make it so, and pass that on.
This is another angle to approach the question, but it may not be valid.
Good luck & happy computing! 🙂