The CHD18x2 supports 3D signals, but it does not separate left eye and right eye and outputs it on the two SDI outputs. 

The reason is, that the second SDI output is looped from the first output and carries the same signal.

A 3D HDMI signal (e.g. Frame Packed 3D) is converted into a SDI 3G Level-B Dual Stream Signal.
I.e. the left eye information and the right eye information are mapped as two HD-SDI streams and combined into one physical 3G-SDI signal.
It is not possible to choose into which stream which eye is embedded.

The specific standard of the outputed 3G-Signal is:
SMPTE 425M Level B – Mapping of 2 x SMPTE 292 HD-SDI Interfaces into a SMPTE 424M 3G-SDI interface.