We have solved this by creating a hosts file on both machines that resolve to the other machine's IP addresses. 

The Laserfiche server still needs to phone home to the License manager at least once every 3 days or it will become an invalid license. When it communicates it assumes the other machine is on the same network so it will only use the first part(s) of the FQDN but will tack on the wrong domain at the end. An example of this is LM.foobar.local and server2.fizbee.local. When LM or Laserfiche try to communicate with each other they'll use server2.foobar.local and LM.fizbee.local

We have gotten around this by placing a HOSTS file that has server2  Ip.address.goes.here on LM and a HOSTS file with LM  ip.address.goes.here on the server2 machine. (and obviously opening up the connection between these two machines)

Now this does NOT allow you to use add named users on your License Manager server. You will need to assign licenses down to that server only.

We've successfully used this in a few different places. The most common need is in a county government situation where they may have a larger entity purchase rio and a smaller entity within the county with their own IT piggyback off of that purchase. Sometimes this is also needed for legal reasons, as funding between the entities needs to be kept separate.