Hope I know what you're referring to... [edit: rereading your post, I probably don't.]
Media Center's database/library contains lots of references to filenames. If you move or delete these files using some other program (like Windows Explorer), links to them will be broken. The X-icons next to those rows signify broken links. If you try to play one of them, MC will just skip them and go on to the first non-broken track.
So if you rearranged the files on your hard-drive, you'll have to re-import them (and remove the old references). This can be done using "Tools/Import Files...", or possibly by navigating to the files in Explorer and doing something on the right-click menu. You can remove the old broken files just by selecting them and pressing Delete.
If you're saying that you re-ripped the CD with new options and then manually deleted the old copy outside of MC, all you need to do is remove the broken links. The newly ripped copy should already be in MC's database.
I'm not sure about the CPU usage, but I hope it's not an issue once you get your library in order.
(By the way, MC has a nice "Rename Files From Properties" tool that you probably should have used. It's under "Library Tools" on the right-click menu.)