Updated to Xcode 4.6 and has strange problems with XiB

upgraded to Xcode 4.6 today and opened one of my projects and got smeared with this lovely error.

* Error compiler interface Builder XiB. The Builder could not open the document "ViewController_iPhone.xib" because it does not exist. *

Going to MyProject / en.lproj I can still see the ViewController_iPhone.xib file. The last thing I used on this project was last Friday under xcode 4.5 and I built and distributed the project and 100% knew the project was ok. I have since gone back and accessed 3 different project backups and all 3 give me the same problem.

Now that it gets even weirder. If I open the ViewController_iPhone.xib file myself with xcode, the view interface popup appears, this is about a 4 month old version of my .xib, however I went and opened a ~ 8 month backup when the project was WIP and it loads the most recent XiB.

I removed the ViewController_iPhone.xib link from Xcode and manually added it back, however the application exits on startup with the error "cannot load NIB in package" and if I close and reopen the project Xcode lost mine. xib again.

A bit more to add, before hitting the Post My Question button, I thought I'd give ti one more try and copy and paste a new copy of the backup to my desktop and open it up, and that's exactly how it was supposed to be! But then I decided to close and reopen the same project and it gave me the same thing that the file doesn't exist.

More information: Mac OSX 10.8.2 Xcode: 4.6 (4H127)

I am really lost on what is happening here and how to fix it. I tried looking for people having similar problems and I couldn't find anyone else who had this problem.

thank