If you have audio tracks only and Sonar keeps going, then there is something there. Get to the end point you want, highlight all the tracks and to the end of wherever it is by the From Now Thru End - and Delete everything using Edit and hole left by whatever it is.
I bet the cursor will not keep going after that when saving and playing the song again.
I bet it even works for Midi tracks also.
No, there is something there, something did not get deleted.