I've got a Keynote file which definitely uses only 3 fonts. All 3 fonts are installed in Font Book.
Every time I open the Keynote file, Keynote comes up with a missing fonts warning. I never used these fonts, so was curious. Duplicated my document, deleted ALL slides and master slides apart from one blank white slide, saved document. Reopened the document. Fonts are still missing.
Can anyone please help explain the problem?
Had the same issue for the past few days. The only solution I could make work:
Export as PowerPoint, reimport, save as Keynote again. Prompt disappeared. Voila.