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You actually can't really control it in the PDF export settings..... at least not completely. Most likely, the strokes are being converted due to the transparency flattener settings (edit > transparency flattener presets). You can choose which preset you want to use within the PDF export settings. I believe that, by default (depending on which PDF preset you use), the medium resolution transparency flattener setting is selected. (oh, by the way, in the PDF export settings, the transparency flattener choices are in the advanced pane). And, by default that flattener preset will convert all strokes to outlines, thus giving them a fill. If you opt to use the high resolution flattener setting, it's not set up to do that by default. It keeps all strokes as strokes. So, it should solve your problem.
Hopefully this has helped some.... hopefully you can understand my gibberish too..... I imbibed a tad too much Grey Goose last night and I'm kind of thinking backwards and inside out this morning. Happy Friday.
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