I'm sorry that you ran into trouble with this. Some users have reported an issue in the current version of InDesign and other CC apps which can temporarily deactivate installed fonts. Please note that this is actually unrelated to Typekit; it just happens to occur at the time you see our logo in the missing fonts window.
The InDesign and app teams teams are still investigating the factors which trigger this situation, but the basic issue is this: the Missing Fonts dialog causes fonts which are managed through Extensis Suitcase and FontExplorer to not auto-activate correctly, or for managed fonts to even be visible in the application after upgrade.
In both cases, the Missing Fonts dialog appears to override the Font Management tool dialogs that allow users to manage fonts within the Application.
If you use Suitcase Fusion, there is a simple configuration change needed:
1. close the Missing Fonts window
3. go to the Type menu and select "Suitcase Fusion 5".
3. From the submenu, choose "Library" and then check "All Libraries" so all fonts can be auto-activated as needed
4. from the Type menu, select "Suitcase Fusion 5" again, and then "Check Document’s Fonts" to activate the missing fonts,
If the font is being managed by Suitcase, it will find and update the fonts.
In FontExplorer, if your managed fonts are not visible in InDesign after upgrading to InDesign 9.2
Go to FontExplorer/Tools and select
1. Clean System Font Caches (this will require a system reboot)
2. Clean Application Font Caches
On non-Mavericks systems, you will need to de-activate and then reactivate font protection. Launch a terminal window and enter
sudo atsutil fontprotection -off
sudo atsutil fontprotection -on
Relaunch the app. your managed fonts should now be visible and auto-activation should work.
The fonts can always be activated from within the Font Management software itself, even with the missing fonts dialog open.
The InDesign and other app teams are looking into the issue to determine the root cause as well; our apologies for any inconvenience it causes in the meantime.