When I got my Linex the guy told me they are the ones who fix factory spray ins for warranty, thats in Michigan, but would guess the franchise would be the same wherever.its a plastic emblem thats double side taped to the bed before the liner is sprayed in..
not sure what they'd do under warranty, but the liner is easily pulled up and could be redone with LineX or whatever popular spray in is used in your area.
id want it fixed too, but when LineX does their process the emblem is usually removed.. so something to think about, maybe contact LineX and see what they say so you have some ammo before going to the dealer.