Here's my thoughts, I do not have experience with furnace systems - it's hot down here!
There's alot to consider in your system. With the new addition was there added glass and type, added space that may no longer be under (or over) conditioned space, orientation (if the addition now projects further than the original structure). If any of these conditions are altered enough it could create a different heat load on the structure. If there's alot of glass added like a curtain wall you may want a professional heat load analysis done so you can make the best decision.
When we size A/C systems down here as a business practice we never max the unit out, usually shoot for about 80-85% capacity for the given load. We use a ductalator to size the ducting for about .08-.1 (drag coefficient I think as my ductalator is in the office) through the duct. We shoot for this number to minimize noise and maximize air flow. As much as possible we'll take a main trunk out full size as far as possible, then size the branches to the spaces looking to minimize the branch run.
Don't know if this will help you but it might give you food for thought. Hopefully one or two of the furnace experienced guys will give their input.