Defining a flex bus in Eagle
A PCB fabrication house I am familiar with treats such "hybrid" board designs as two PCBs, with the junction as an array of traces on each side, to be soldered as per their normal process. This is similar to how a regular FFC would connect to a regular FR4 PCB. 

The board files, including copper and mechanical outline layers need to be separate for the two PCBs, with annotation to indicate alignment for assembly / soldering. 

Other fabricators might offer different options, though it seems a little unlikely that a single board file would be accepted: The actual FPC and FR4 boards would be etched and routed in separate processes, so combining the design into a single board file leaves the separating out of the two parts into separate outline, copper, resist etc in the hands of somebody at the fab shop.