Sorry for the late reply, I haven't been here for a while. You can use an Acrobat Preflight Profile to flatten the annotations into the page content- Tools> Print Production> Preflight> Flatten all annotations into page contents.
Re: Convert stroke to fill in Indy or Illustrator CS2
You could also do this with layers- the shape with the fat stroke on the bottom, the other shape above that, then the first shape, but without the stroke.
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