Were the files available for download before the first sync attempt? Might be that when the first sync failed the changes were rolled back and somehow you lost the files there...
Have you got more information about the missing FileDocuments on the sandbox environment?
In my app, running in the sandbox, all FileDocuments are missing too. New created FileDocuments are available for download, but FileDocuments from the past are all missing.
Are FileDocuments removed in Sandbox environment by Mendix periodically?
did you manage to tackle this situation, since we are having exactly the same situation, where it block several users from completely starting their app.
It would be greatly appreciated.