Every night my machine disconnects from the Control Box

 RobOntario Talk to your IT department. Sleep settings can be enabled in the BIOS too. Saw this at another customer recently where all the power saving options where turned off but there was a bios level setting that had been enabled that was putting the machine to sleep. You can also check Windows event viewer to see if the machine is being put to sleep.

It's a long shot but it may also be worth checking the controller settings.  Some of the newer FDC controllers have "Eco mode" settings that are designed to put the machine to sleep after a certain amount of time if it isn't active.  Saying, that, I believe it's designed to power up again as soon as somebody interacts with the machine (by moving the jogbox or trying to execute a routine for example).  To access the FDC control panel, open a web browser and enter 100.0.0.1 into the search bar.

It's a long shot but it may also be worth checking the controller settings.  Some of the newer FDC controllers have "Eco mode" settings that are designed to put the machine to sleep after a certain amount of time if it isn't active.  Saying, that, I believe it's designed to power up again as soon as somebody interacts with the machine (by moving the jogbox or trying to execute a routine for example).  To access the FDC control panel, open a web browser and enter 100.0.0.1 into the search bar.

does the eco mode then disconnect from the machine from the license? 

I'm not sure because I've not worked on many machines that have it.  I would think it just powers down the servo's.

No, ECO mode does not disconnect the machine from the computer or license.

If you run this command in administrative level command prompt it will generate a sleep study showing you how often and when your PC is being put to sleep.

powercfg /SleepStudy /output %USERPROFILE%\Desktop\sleepstudy-report.html

This will generate a 3 day study of power actions on your computer, it's pretty detailed.  You can use this to determine if and when your CMM computer is going to sleep and bring it to your IT department.

it can also be power fluctuating for the PC, it will disrupt the Ethernet port and cause it to drop off. if you have an adaptor Ethernet to USB, that can cause it to drop off as well due to issues with the USB ports. BOXX had problems with this in the past.