Yes.. when you lift the rear you change your caster.. as you change the caster your Toe will change since a different part of the tire is now facing foward.. It could even throw off the camber..
Also, if a shop won't touch it, or waranty it at least for 90 days find another shop. If a shop knows what they are doing it can be aligned.. If it can't (i.e. you have 2" lift, and no drop brackets that is possible) they can at least get it as close as possible.. They would be able to set the toe and get the camber as close as possible.
~Mark