We added a great room and 12 foot on to the existing kitchen. I am planning to install radiant heat to entire first floor - great room, new kitchen, existing kitchen, dining room. I purchased a thermalboard that allows me to install the radiant heat on top of my subfloor (existing and new addition). My problem is the new kitchen addition is "level"/flat to part of the existing floor and my existing floor is sagging toward the center of the house by approximately 1.250" in 9 foot. Will this be a problem if I install a floating engineered floor?:?

Yes, it is a big concern.

Substrate flatness requirements are very strict!!!

1/8 of an inch, in a 6 foot radius, is the universal standard. Manufacturers can and do set there own specs.
OwensPlank is 1/8 in 8 feet