Sorry to hear that you are experiencing issues with the integration of ArcGIS Urban and CityEngine.
The integration between the two products is currently under development to provide a more seamless data exchange using the new ArcGIS Urban API, so what you are experiencing since the release of Urban is expected and a known but temporary limitation.
We are working tidiously on finding a solution and will keep you up to date on our progress. We can ensure you that the integration is going to be working again, but cannot confirm yet when exactly. We apologize for any inconveniences.
Feel free to reach out at any point with furter questions.
Thanks for reporting that you are seeing issues with projects as well. This is also unfortunately expected and we are working on fixing it.
For design projects in particular, you could try to use the general feature layer sync by connecting to the urban design feature service that is hosted in your ArcGIS Online portal.
Hope that this might solve your issues temporarily. Thanks for your understanding and sorry for any inconveniences.