This used to be an issue in Indesign as well as illustrator. Indesign has fixed this issue since it would fail a pdf export.
The main problem I run into with this issue is that the Output Intent in PDFs are written out as "Modified" and creates downstream issues when Indesign and illustrator PDFs are combined on a single press form when the output intents do not match.
The additional issue in illustrator is using a modern version 4 profile (modern as in 2013 GRACol CRPC's) will force a version 2 ICC profile conversion and force a dialog response. Any automation such as javascript or AppleScript will require user intervention.
This used to be an issue in Indesign as well as illustrator. Indesign has fixed this issue since it would fail a pdf export.
The main problem I run into with this issue is that the Output Intent in PDFs are written out as "Modified" and creates downstream issues when Indesign and illustrator PDFs are combined on a single press form when the output intents do not match.
The additional issue in illustrator is using a modern version 4 profile (modern as in 2013 GRACol CRPC's) will force a version 2 ICC profile conversion and force a dialog response. Any automation such as javascript or AppleScript will require user intervention.