Yes I had a very similar experience as the original poster last week when I more or less did the same thing. My first disappointment was that there did not appear to be any reference to what a corrupt project is, what causes it and how to deal with it in the manual.
I created a folder on the desktop called MIDI and another called Audio. I then revisited the project file that I had copy and pasted the 2 corrupting files from and exported them to the empty folders. I renamed the corrupted project after removing the material I had pasted in and saved it. Then I imported the files from the desktop into the project to 2 new tracks 1 audio and 1 MIDI that I had created. I was then able to save the project.