After I save an Illustrator file to a PDF format and then try to "autosave" the document, Illustrator saves it as a PDF instead of overwriting the .ai file. This causes problems for me because I save PDF's without editing capabilities, I would like to know if there is an automated way for Illustrator to save to an .ai file instead of overwriting the pdf.

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If you want to keep the Illustrator file open and still save to a PDF make sure you do File -> Save A Copy...

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