This might sound silly, but if they did not print a revision to correct the mistake, you would probably need a Train Order.
They did have rules in effect, the Train rules. What was not in effect were the Block and Signal rules. The Train rules are always in effect on main track and are the basic rules. Train rules set superiority, representation, flagging, time zone, how long to be on the main and a host of other basic functions. They use the Special Instructions to implement where necessary, Signal and Block rules to supercede or coincide with the Train rules where applicable.
They could run, but it would be like it was in the late 19th Century and I would think most are not acclamated to that kind of environment. The single track territory is a perfect environment for operating under Train rules only. If the crews really knew their stuff, you would even notice the Block and Signal rules were not in effect.