Amanda,
If there are any hyperlinks from the topics in the new CHM to
those in the old CHM then, when you compile the new CHM, the help
compiler tries to pull those old topics into it. But because those
topics are "above" the root of the current help project, they'll
get stored in the wrong place within the CHM. This means that they
will show up in the results of a search, and if they contain any
embedded index keywords then those will also show up in the index.
Yet all links to the topics will be broken.
You should be able to verify this by using a tool like
KeyTools (
http://www.keyworks.net/keytools.htm)
to peek inside the CHM. You may find that some of the old topics
are visible using KeyTools' Examine CHM feature.
I'd recommend removing from your hard drive anything that
isn't needed to compile the new CHM, as this will ensure that the
compiler can't drag unwanted content into it.
Pete