4.6.1f1: Can't save scene

I am working on an old, complex project with numerous plugins. After upgrading to 4.6.1f1, neither myself or my other teammate are able to save scenes.

This is really, really bad for a live app!

I am working on a new Mac running OS X 10.10.1 (Yosemite). He is running Windows 7.

We both verified the issue by:

1. Creating a new scene

2. Saving the scene (this worked, oddly enough)

3. Renaming "Main Camera" to "Main Camera 2"

4. Saving the scene (via the file menu). The menu bar icon does not indicate the scene has been saved. There are no errors.

5. Re-opening the scene

If the system was working correctly, the camera should be named "Main Camera 2". But it is still "Main Camera".

The following "workarounds" also did not work:

1. Opening a new scene and forcing a save

2. Quitting Unity and forcing a save

3. Opening a new project and forcing a save

4. "Save As" the same file

It IS possible to save the scene as a different file! Which is a PITA for version control, but at least we're not totally sunk. Right? Right? -_-

We verified it is a project-related issue by creating a new project and running the same test, with no errors.

According to forum searches, there are two possible explanations:

1. OS Issues

2. Plugin problems

It's not an OS issue if it happens on a new Mac AND a version of Windows. So it's probably a plugin issue. But how to identify which plugin? And if we wanted to (ugh) remove all plugins and re-add them one by one, how would we even begin to properly remove them entirely? This is a very, very complex project that's had several lead programmers. It would be a nightmare. It might not even be possible.

Looking for help. If you have insights or suggestions, please share. Thanks.