Without seeing your home, my best advice is to seek a more experienced dealer. A one man shop does not fill that bill. You need to know the various options and associated costs before closing on this property. Just from your short anecdotal story, I probably would pass on this home.

IMO

One idea is to add a mini split system...

Here is a link that might be useful: Ductless Mini Split Systems

tigerdunes -- wow....I didn't expect to hear that we should pass on the house! I appreciate your input but I'm wondering what makes you say "pass" right away -- are you in the HVAC business and know that there isn't a good way to deal with this?

Yes...to your question...

You asked...I answered.

You need another expeienced dealer to offer suggestions, options, and associated costs. Money solves a great deal of problems. Depends on how deep your pockets are. I really don't understand why the two systems were setup the way they are. See my suggestion and link to a mini split system.

And yes, passing on the house should be a worst case scenario. I would not close on this property though until you know the full range of options and their costs. The ideal situation would be a separate system for upstairs and downstairs. What is the size of each zone? Tell us exactly what HVAC is in place now-brand, age, mdl numbers, size, etc....

IMO

upstairs rooms that have walls that are shared with
attic space are always difficult to condition.
hot in summer...but in winter heat from downstairs
makes it easier to heat.

in my experience it is the walls themselves that are
the cuplrit...not lack of hvac.

attic temps are extreme. in the summer the attic temps
can pass 130 degrees. R-13 batts in walls just doesn't
stop the heat transfer.

you can throw more money in hvac at the area...but
it will be at a preminum cost, both in equipment and
costs to operate.

fixing the walls is a one time cost. then conditioning
the space is achievable.

walls shared with attic should be insulated. usually
batts stapled in place, in full contact with wall, and
no gaps or voids. then a foil faced foam sheathing
board, nailed to the faces of the studs.
foil faces into attic space to reflect heat out of walls.
install is with button cap or roofing nails. sheathing
is caulked to studs, top and bottom plates & all
seams are taped.

this install both insulates and air seals these
problem walls.

do a site search of FROGs family room over
garage...to see that these are common problems with
rooms that share attic space.

southface inst has great detail in their air sealing pdf
linked below...page 5

http://www.southface.org/default-interior/Documents/airsealingkeypoints.pdf

best of luck.

BTW,what is your location and age of this property?

IMO

I do agree with energy rater. I would call an insulation contractor out to tell you exactly what you have, what can be done to improve,and the costs. Good DP windows upstairs?

IMO