Since updating to 4.6.1f1, my teammate and I are unable to save changes to existing scenes (though we can create new ones), and we can’t save changes to prefabs between sessions (meaning: we can update a prefab, apply the changes, and see those changes during the current session, but if we save the project and restart Unity, those changes are gone). This also affects import settings of textures and the like: they are not saved at all.
He is running Windows 7; I am running a new install of OS X 10.10.1 and a new install of Unity.
Oddly enough, new scenes can be created. So, where in the pipeline something is going wrong is not clear, but there are no errors in the console.
This is a project-specific issue, and likely due to a plugin. I have verified that other projects which are otherwise identical (i.e. Github source control, 4.6.1f1, etc) do not have this issue.
My reading on the problem indicates it emerged in 4.6.x, and was fixed in some cases. Other people fixed it by removing plugins. However, pulling out our plugins one-by-one to discover the culprit is not an option – the project is too complex. (it might be possible if Unity had a standard way to add/remove plugins, but no, everybody likes to be different)
Regardless, the fact that these problems were introduced in 4.6.x tells us this is a Unity issue, and we would like to hear what is going on at Unity HQ to address it. We’re willing to send the project over if the necessary paperwork gets signed. This is a bad, bad thing for us and several others.