If you wanted to remove them, you would remove them from the Database.
Though, the easiest solution would be to make use of the spells import/export scripts. You can run those scripts to either export all of the spells in the database into a spells_us.txt file that you can put in your EQ folder, or you can import the spells_us.txt file that you currently have in your EQ folder into your database. Either solution will work and will get rid of the unknown spells. The main point is that you need to have your server and clients matching spell files.
The downside to removing spells from the DB is that you would probably be removing focuses and other spells that higher level items use. As long as you don't plan to use newer items, you shouldn't need to worry about it, though.
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