Export PDF that is totally CMYK compliant

Hi, I'm using the PDFX1A settings when exporting from Indesign. My PDF is CMYK when any RGB images are used, which is what I want. But if I have an illustrator eps that uses spot colour (logo) linked to the the indesign document, that doesn't convert to CMYK on the PDF. How do I get a total CMYK PDF. Opening and converting source files is not an option in the workflow.
Thanks, Tim

Tim, I just noticed you need to skip keyline so it would be:
tell application "Adobe InDesign CS5"
activate
set myDocument to active document
tell myDocument
set docInks to inks
repeat with x from 1 to count docInks
--you can skip an ink via scripting
if is process ink of item x of docInks is false and name of item x of docInks is not "keyline" then
set convert to process of item x of docInks to true
end if
end repeat
end tell
end tell

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