The rules cover this too. If there is already a person protecting the crossing, called “flagman” on my railroad, trains won’t have to stop and protect. A stop and protect order is it’s own separate thing.
We will be informed of the situation either in our initial orders or over the radio and then copied to a paper form. If it’s in our initial orders which means they know about it before, it will generally read “crossing protection at Anystreet ,M.P. 123.5 out of service; flagman yes” This is usually for track or signal work that is know in advance.
If we get one over the radio the dispatcher will say “activation failure flagman both directions yes”. The conductor will hand write this on a form to keep a record. This is common when trucks hit the gates or signals.