When a mixed RGB/CMYK PDF is opened in Illustrator CS6, Illustrator forces a conversion to one color space or the other. See this screenshot: http://imgur.com/sK8iEdn
I assume this is a limitation of Illustrator and there's no way to keep both color spaces. Under that assumption, Is it possible to choose the profiles used for the conversion from RGB to CMYK? Can Illustrator be made to use the RGB and CMYK profiles defined in its Color Settings to make this conversion?
I did some experiments with Illustrator CS6 and the MacBeth RGB test chart and verified my results with Photoshop CS6. I discovered Illustrator is (mostly) doing what it should be doing, within a 1% error (probably rounding) on the output CMYK values. Here's a summary, in case anyone else needs this info:
Assuming the source file's elements are all untagged, when a mixed RGB/CMYK PDF is opened in Illustrator and CMYK mode is
chosen, Illustrator will use the profiles and rendering intent defined in
Color Settings to make the color conversions from RGB to CMYK. Thus, we
have control over the profiles used for this conversion.
If the RGB elements in the PDF file have embedded ICC profiles,
Illustrator will use the embedded ICC profile instead of the RGB profile
defined in Color Settings. This ONLY happens, however, if the PDF file
also includes the correct CMYK output intent profile.
If the PDF doesn't contain a CMYK output intent, Illustrator will fall
back on the Color Settings RGB profile for RGB->CMYK conversion. I believe it
would be more correct for Illustrator to use the embedded RGB profile and
the CMYK profile defined in Color Settings, but that's not how it seems to work.
If the PDF contains the incorrect CMYK output intent, Illustrator will
ignore the Color Settings and respect the embedded RGB and CMYK profiles
for the conversion, as might be expected.