Does that project you copied back to an internal drive have its audio clips within the Audio sub-folder of that project file, or is it possible the audio clips are all back in some common folder.
I am just sort of wondering if the project file is looking for the audio from back on the external drive, where there is some sort of timeout being determined by Sonar, in accessing data from the slower drive.
I wonder if you would still get that error if you created a simple midi-only project and after saving it, moved it to the external drive and then tried to open it again from the external drive. This would just test to see if the audio data is at the heart of the issues, in some fashion.
Separately, is it possible that Windows is using Selective Suspend to disconnect the external drive? Windows default behavior will conserve power by 'turning off' idle USB-connected devices, after a certain amount of time.
I always modify that behavior in the Windows Power Management advanced options, to disable that feature, as I have USB-connected midi controllers and my audio interface is also USB-connected.
Bob Bone