I don't think you need to enter an upper-case y because I never have. It's not really a good idea to run apt-get upgrade at all, they told me. I've been running it anyway and never got burned.

If you really care that much, you could disable a bunch of repositories and see if you still have the problem, etc, and use that sort of process to find out what repository is causing the problem. I would probably just not run apt-get upgrade for awhile, in reluctant respect of the advice I got...