The best practice is to consult your printer first. Some printers actually prefer the color swatches stay Pantone because their RIP can automatically do the correct conversion at output. Hi, yes this printer wants the colors converted to CMYK before they get them (and that has been my experience with most printers).
While most colors are convertible from RGB to CMYK, if there are any noticeable color changes during conversion, you may need to revisit a step and adjust some of your values before converting. Inconvertible color swatches that cannot be replicated accurately in InDesign or Illustrator will appear in the preview with a yellow warning triangle
Since you have access to Illustrator, you might want to try importing the PDF into Illustrator and using Illustrator's scripting capabilities to iterate over the elements and replace fill/stroke RGB colors with their CMYK replacement colors.
The template (the branding etc) is produced by Illustrator in CMYK - the 2 text panels either side are imported from an external database and linked to the template in Illustrator. We also need to batch convert as we have a high volume of labels to produce. Also when the database is updated with new information, the linked text panels in
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how to convert rgb to cmyk in illustrator
