You are probably saving the "Illustrator" file inside of the PDF.
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When one saves a PDF file, the current (i.e. 12) and recent versions of Illustrator do save Illustrator documents
inside a PDF file, BUT in fact, the Illustrator editable information is saved as private data in the PDF file. In saving an
Illustrator document, you do have the option of creating a file with true PDF data, in which case you can actually open
up the .AI file in Acrobat or Reader. Conversely, there is an option in saving PDF files from Illustrator that allows you
to save the Illustrator edit information in which case you can fully and properly open the .PDF file in Illustrator.
In the general case, if a PDF file is not created by the same or earlier version of Illustrator and does not have the
“private data” describing the document, opening a PDF file in Adobe Illustrator results in a potentially lossy
operation. Adobe Illustrator does not support all features and options of PDF. Mixed colorspaces and other
features not supported by Illustrator will result in data and/or features from the PDF being discarded without
specific notice to the user.
A comparable situation exists with regards to both EPS (Encapsulated PostScript) and PostScript files.
In the case of EPS, Adobe Illustrator can only fully and properly edit EPS files created by the current or
earlier versions of Illustrator. (dov)
MSD