I just ran into this issue running AVR Studio in Parallels on MAC OS X.
If you compile you code and then run debug (AVR Dragon)
Once you stop the debug and try to recompile, it complains that the .elf file is missing.
If you restart avr studio, it compiles again.
The problem is caused by using the //.psf shared folder.
I found, if you rather use the z: which maps to the same folder, the problem is solved.