I've had this happen a few times.
The contents of proj.xcdatamodeld/proj.xcdatamodel/ randomly disappear off my hard drive. However, Xcode will open the model file just fine.
Sometimes all three files disappear (elements, layout, contents). Other times only a subset of the files disappear.
I've done a filesystem check with Disk Utility which detected no problems.
I've checked that all the build settings etc. for the xcdatamodel are correct.