I haven't unlocked/rebuilt the Battle Machine yet in CoC Builder Base.
Since the Master Builder "operates" the Battle Machine during an attack, can you use the Battle Machine for attacking when the Master Builder is busy upgrading a building?
If so, does it halt the Master Builder's upgrade of the building during the attack?
No, Master builder continues building's upgrade. That means him, fighting in the battles via the battle machine is a separate matter of him upgrading.
I checked this by the remaining time of the upgrade before and after the attack, It's not halted during the attack.
Took a look at what the CoC wiki has to say about the battle machine and it doesn't say anything about the Master Builder not being able to upgrade buildings when it is in use, nor does it say the battle machine cannot be used if the MB is upgrading something.
However I have yet to unlock it as well, so I cant add my personal experiences to this answer.
