I have placed a pdf in illustrator that has embedded subset fonts. In illustrator the fonts display wrong but I get no warning that fonts are missing. When I click on the substituted font the type panel shows it as the correct font name. Are there any cases of a file with missing fonts not displaying a warning? If I save the file and reopen it I do get the font warning.
Possibly there are different versions of the font. The name may be the same, but the document could refer to an older/ different version and only when you save does that info get updated. Hard to tell without actually seeing the Doc. What does Acrobat say exactly about the font? Is there a doifference in that info when you re-create the text locally from within AI and save a PDF with the same options?