I'm thinking of playing a lester in my next game, and I'm wondering will he lose the ability to confuse after he gets the special song HLA?

Yes.

Do a Google search for the Rogue Rebalancing mod. Its "Bard Kit / HLA revisions" component . . . um . . . revises the various Bard kits and their respective HLAs, including each kit getting their own Enhanced Bard Song, a more powerful version of their original Song.

Don't install the Shadow Thief Improvements component, though, and be very wary about installing the Chosen of Cyric Encounter.