botnetop.tcl wipes them, as they caused problems mainly when switching from from getops (or another opping script that uses need-op, etc.) to botnetop.tcl. I consider the need-* chansets a legacy thing.
With eggdrop 1.6 you should use need binds, which are stackable and don't get stuck in the chanfile (so you can get rid of them with a .restart). Refer to tcl-commands.doc for info on need binds.