I recently have been in contact with Unity support regarding an issue with a project that was using Unity Collab. At some point during an editor version upgrade the data in the cloud became unusable - Unity support said that they had a lot of 'Broken text PPtr in File' errors.
Unfortunately, there wasn't a fix for this - all fresh clones of the project had broken links to scripts (Scenes, Prefabs). The only solution was to make a fresh project and link the working copy of the project to it. For me, this wasn't an issue but those who have much larger projects using multiple Unity services creating a new project wouldn't be an option.
My suggestion would be to add the option to purge the collab data using the developer dashboard. Currently, all you can do is archive the entire project.