I faced the same problem. My problem was that I could modify a file, but not another (both are in same project). Later I found that the file I couldn't modify was also part of another project. That another project (Unit Test) wasn't loaded, and intelligent VS debugger shows the error that assembly for this given file was not loaded, and changes aren't allowed. How weird!
Hence, I had to unload the unit-test project and continue the EnC debugging.