With regards to contingency plans being thought through - the thing is, the normal timetable isn't running to the final plan at present. How Thameslink services should be run, is that a Driver works a service from end to end for the most part. This isn't happening with a significant number of services that run to/from the GN having a change of driver booked to take place at Finsbury Park - with mostly, them working the next train back in the other direction 20 minutes later. This is because route training has not been completed.
Any contingency plans drawn up when Thameslink was planned, have had to be altered (probably for the worse) to take into account the current situation, which Is different to how Thameslink should be working.
With regards to the train with a dragging brake in the core - the wheels would need to be examined to see if there were flats on the wheels and if there were, how bad. This would need the adjacent line blocking to check the wheels on that side of the train. Boom, there goes your 4 trains an hour on that line for the duration of getting the block put on, driver climbing down onto the track, walking on ballast to the affected coach, checking the wheels, walking back, climbing back onto the platform and getting the block taken off.
In addition, if the flats were deemed okay for the train to be moved, then a rotation test would need to be carried out, observing the wheels rotating round after the affected brakes were isolated.
Brakes - if it's the parking brake, this needs release pins to be pulled on both sides of the train. So we've got a lack of access on one side due to platforms and tunnel walls, and having to block traffic on the other.
You can see that the block on the adjacent line could be on for longer, or take place multiple times. I'm not at all surprised it took ages to sort out.