Hi @wolfi,
Saw your email that you downgraded to 1.4.9. Can you try this again for me? This time, try to unsync the parent folder/s of the affected (missing) subfolders then resync. Please let me know if the issue persists.
Again, I’d like to sincerely apologise for being unable to provide an immediate fix to this. 
As mentioned in my email, our engineers are currently focused on rebuilding the app’s core for a more seamless user experience. We completely understand the frustration especially for users like you who are heavily reliant on Insync for work. Rest assured that the support team is working closely with our engineers and we’ll give an update as soon as possible.
As always, feel free to reach out for any other questions or concerns. 