Cyclone V LVDS differential termination

Sounds unlikely. Up to now, the basic method with differential I/O standards has been to assign the non-inverted pin and also specifiy additional I/O features for thi spin.

The pin planner tool is primarly a wrapper around the pin assignments, but does some things on it's own by e.g. displaying the inverted pins along with the (primarly assigned) non-inverted pins.

In case of doubt, I would check the actual pin assignments, in assignment editor or *.qsf file.