In one document I have a bit of text in Orbitron Bold, from typekit, and InDesign claims the font is missing, however every other document has Orbitron and are not complaining.
Orbitron appears in my list of installed fonts but when I select it, it immediately jumps into the square brackets to say it's missing.
The automatic typekit sync thing says "Typekit could not find any matching fonts."
I'm on Windows 10 with InDesign CC2015.0 (but only because the CC app isn't telling me that there's an update, which I know there has been.)
Not sure if this will work or not, but I guess it's worth a try.
In your Creative Cloud desktop app, go to Assets > Fonts.
Click the Manage Fonts button and press remove for the font in question.
Then reactivate the font by pressing Use Font button on the Typekit page.
If you go to Type > Search Font, does it show you which style is missing, not only the font? Maybe that you use a style which is not included with that font. It could also happen, if you apply a character style—maybe automatically via nested styles, GREP styles, automatic numbers and bullets— which includes a style definition only, which is your font different named.