Sounds like they either had to get switches in hand(legitimate reason for the excessive delay) or the RTC was trying to play the "blame game"(an illegitimate reason).
If there has been a 439(pass stop) violation - either crew responsible or a "technical"(system fault) the RTC will immediately get an alarm on their panel. They must then immediate contact the crew and confirm the situation in the field. If the crew states the signal dropped on them the RTC shouldn't waste any time dilly dallying and should issue a pass stop(rule 564) immediately. Most RTC are quick about it, but some like to be accusatory and waste time unnecessarily questioning the crew, in essence trying to find some kind of fault with the crews actions in self serving attempt to absolve themselves or CN of any responsibility. I am speaking from personal experienced having gone through this a few times myself.
Meanwhile the conditions of a "pass stop" allow a train to enter and pass through a signal block safely. Copying the form takes some time as does going through the block at restricted speed(15mph maximum). However if the crew has to get "switches in hand" that would of required them to stop before every switch in the controlled location, take it off power, reroute it for the route to be used and then have the train pull up directly on top of the switch before putting it back in power. The "dual control" switches used in "controlled locations" are not easy or quick to use and would explain the larger than normal delay.