An associated question. So, the commands baggage is also considered lost. I assume then that it has to be removed? If so, what happens if you have say all six Bge(O) elements based as one solid 3 x 2 element block like most people I know do?
If it's command baggage then it has to be in the deployment rectangle for the command, which makes a singel 3x2 block highly problematic for 3 commands - not impossible tho - the middle one could be deployed in a 1-element wide column directly in front of the baggage!!
If it is command baggage and legally deployed like that then there's stil no problem - the 2 baggage of the broken/shattered command counts as lost, the rest does not. If it is immobile then it stays there, if mobile then it flees.
Most such blocks of baggage should be representing army baggage tho, which is a different thing altogether since it is all in a single command, and counts as lost only when that command is broken (or when destroyed in combat of course).