The limit was set by our manufacturing manager to limit the complexity of cutouts submitted directly through the PCB123 software. Any complex routing the cannot be drawn the the PCB123 provided tools should not be submitted through the software. These jobs can then be directed to the appropriate Full Feature or Custom Quote service.
The delays you experience refreshing the layout is likely due to the complexity of the polygons on your layout and not a result of changing a pins properties. At this time the more complex your filled polygons are the longer it takes for PCB123 to draw and redraw them. We are working to improve this for a future release. A work around is to view your polygons in wire frame mode after you drawn them. This should greatly reduce redraw time.