the whole point of an exhaust brake is to push pressure back into the engine and use that pressure on the top of the pistons to help slow the truck down without using the wheel brakes as much.
sounds like your dealership's parts-replacer is confused.
additionally, we call that thing an "exhaust brake" but in reality it's more like a turbo vane brake. the computer uses the variable slider to lock the exhaust side of the turbo into the low-rpm setting to restrict flow through the turbo. a proper exhaust brake is a butterfly valve in the exhaust pipe (usually either the downpipe or as close to it as practical) which impedes exhaust that way. same net effect but more reliable, as the electronics are farther downstream from the engine (since electronics don't like heat).
if you need to leave the EGR stuff for visual inspection, grab a couple dorman freeze plugs and stick 'em in the crossover tube so there is zero pressure bleed across to your intake. however, the most effective way of eliminating the engine breathing its own poo and the associated problems therewith is to completely remove the stuff and tune the engine appropriately.
check out this thread; there's a bunch of helpful info in here when considering which, if any, level of "delete" is right for you:
http://www.cumminsforum.com/forum/0...-3rd-gen-6-7l-powertrain/99081-6-7-egr-test-results-finally-completed-read.html
hope this helps.