If it was mine, I would take the unit out. I wouldn't use the attic for storage and would try not to disturb the area at all once it is well insulated. One of the most important things with insulation is continuity. If you miss 1% of the surface area, you don't loss 1% of the insulating value, you loose 10% or more from the hole (for the whole wall). The same goes for the attic access, the whole attic can be R-50, but if the door in poorly insulated, the R value of the whole attic decreases alot. I would make the access equal to the insulation value of the rest of the attic and essentially seal it off except for emergencies. If you try to use if for semi routine storage, small acts of laziness can ruin all your work trying to improve the insulation.
good luck