That really stinks. If you haven't painted the Oratex underneath yet I would say It will be no problem. So, It seams the DAR believes while building an Experimental you must follow the build manual. I don't believe rerouting Brake lines would be a significant enough alteration/modification to justify putting the plane back into phase 1 after you finish your 40hrs. Rather than address it with the FSDO I would route these his way then when your phase 1 is finished and you still find it undesirable change it back. Unpainted Oratex will patch so easily.