New project can't preview/publish

Summary: We want to create a new project to push through changes through visual builder studio as the default project applications extensions is available across multiple environments and has changes we aren't sure of. We also want to limit what can be pushed through to our live environment so do not want to create the environment links in applications extensions.

The issue is we have created a new project, and then created the workspace using edit page in visual builder. I think because the repository was already being used by application extensions the new workspace does not seem to be created properly. There is no UI App or other menu options no dependencies etc and we can't preview or publish changes we get the following errors