I pulled my stock fender off and replaced it with a CF Sebimoto one when my disc lock took a bite out of it. The retaining "thingy" for the crossover line just sort of "pops" out of the fender, as I recall. Either that, or the line itself pops out of the retainer, etc.
(Oh, yeah, I just jiggled the fender loose after getting off the fasteners and folded its "fangs" inward to get it off)
When I put the new fender on, there was naturally no such retainer (and indeed, there were no holes drilled at all) and I just left the crossover lie loose. In theory, it could fall behind the fender and towards the wheel, but it would take a lot of force and even then I don't think it would get caught.
Anyway, I lived with that for a couple of months and then got dual system SS brake lines, so the crossover was no more. Problem solved.