Illustrator is NOT A GENERAL PURPOSE PDF EDITOR.
Stop using it as such.
Why do you ask it in the InDesign forum? BTW, Bob gave the correct answer.
Is the font installed and does it work properly if you create a new file in Illustrator?
As mentioned above, the only PDF files that Illustrator is guaranteed to open correctly are those made in Illustrator and save as PDF with Illustrator Editing Capability.
You might also want to take a look at the IndyFont script for InDesign. You mentioned you already have Fontographer, but IndyFont is quite versatile and works within the familiar ID interface. http://www.indiscripts.com/category/projects/IndyFont
That's what I get for submitting this late at night -- wrong forum!!A clear case of LMC! (Low Marble Count). Bwa ha ha!
I create music scores in Finale (sort of the Adobe Illustrator of the music world) and want to do additional things to the final score with Illustrator. Once it's in Illustrator I want to do my thing and then save it as an Illustrator file, never to be a PDF again.
Your observation solved the problem. Finale offers other export options, and one of them imported into Illustrator just fine. Thanx!