`xcalib -i -a` controls only one of two screens - can it control both?

Solution 1:

No.

Note that as of date of last testing (2014, xcalib version 0.8) xcalib has not been able to invert the colors on all monitors in a multi-monitor setup, because all monitors are presented by the X11 server as a single screen. Thus this limitation is coming from the X11 server. xrandr-invert-colors does not have this limitation, because it uses XRandR API, which correctly handles all attached monitors.

from here: https://github.com/zoltanp/xrandr-invert-colors

Solution 2:

The display ids in X follow the form :<screen>.<display>. Contrary to intuition, all the monitors in a multiple-monitor setup share a <screen>, but have varying <display>. The screen "first" in the setup is :0.0, and others are :0.1, :0.2, etc. The final command is xcalib -invert -alter -display :0.1