What version number of AE are you using?
Are you still triggering this dialog box in your standard workflow, or have you fixed this issue? Please give us an update and if you need more assistance with this perplexing issue.
did we ever get an answer to this question? Only today have i started getting this error when i open a file that i don't have all the fonts for. "Unable to initialize the sync missing fonts dialog". Then the project wont open.
Running CC 2017.2 (22.214.171.124), OSX 10.11.6
Can you import that project into a brand new project?