Thanks for all the input guys.
It seems that my output was indeed the issue. I just set up a new Focusrite interface, and the projects that I assumed were corrupted are now loading and playing normally again! If I continue to have the same degradation I'll know I have other issues, but as of right now, smiles all around.
I'm in the process of building my first DAW, and kept putting off buying the interface in lieu of other components and plugins. Didn't feel a sense of urgency since my stock sound card and ASIO4All seemed to be doing the job well enough. I didn't realize the output could give Sonar such conniptions. Plus, everything sounds better now. Should have done it sooner.