I believe it removes instances of the items from the dbc files, it doesn't remove the dbc's themselves. It might be more common for users to remove (pull out/delete) all of the dbc's manually then use the Launcher to reinstall only the small number of sims3pack items for which the Multi-Extractor conversion just isn't going to work. I believe that counters (surfaces) might fall into that category as would custom patterns and default skin replacements if they came in that form.
Not the ebc files though, those are your installed TS3 Store content and are encrypted.
But it would probably be better to get some input from players who have actually gone through this themselves. I am sure there are many here, but more on MTS if we don't get enough of a response.
