You can't edit a mobi file (not easily anyway). It's a compiled binary database. You must convert to an easily editable format (or extract the markup using kindle|mobi-unpack) edit that, and then rebuild the mobi.
It's possible that you may be able to achieve what you want through a calibre mobi-to-mobi conversion, but not likely. If you want to delete content, your best bet is to convert to epub/html, delete the content you don't want, and then convert back to mobi with calibre or kindlegen.
EDIT: what Doitsu said.
