Firstly - you don't need to use that button if they're in the levels folder. NL automatically finds anything that's in there (you do need to restart NL if you've added new stuff while it's running, though). It's for if you want to add stuff from other locations.
Anyway, these will be in $LOAD sections near the bottom of the userdata file. If you remove them from the $LEVELS section that makes up most of the file, this only clears your progress and records, not whether they're in the list or not.
Side note - the levels board is not the place for this. That board is for posting level pack releases only; I've moved this to the general NeoLemmix board.