A couple of possibilities. 1. You are using Suitcase Fusion2. SF2 has what's called the FMCore plugin. That plugin activates/deactivates fonts even when you do not have SF2 running. When you close SF2 though it closes any temporarily activated fonts.
2. Even if you aren't using SF2 and fonts are closed when you quite Suitcase you would not get a font warning if you still have the document open, particularly when still processing a job. You only get the font warnings when you open a document, begin printing/exporting a PDF, or when saving out an EPS file.
3. If fonts are not present when a PDF is being created Courier is substituted. Courier is the default font for this. Your fonts went missing during this PDF creation and so the PDF engine subbed Courier.
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