owen_li, as you mentionned the placer could change the flops order along the scan chains, and so conformal tool could not formaly made a equivalency between the two netlists as the pin SI is not driven by the same SO pins.
You need to force scan shift signal to inactive, and the LEC tool will not check the SO->SI pins connections.
The same issue appears when you want to LEC between the netlist before scan insertion and after scan insertion.
To check if the scan chains are unbroken, using this netlist in an ATPG tool could confirm the stuck coverage if it is equivalent as you have obtained with the netlist after scan insertion.