I'm not sure why the dealer in cork told you the control unit would come programmed, i have been working for bmw for 4 years and the only way to programme a control unit to your bike is to have the bike actually there to do it. When you programme control units the diagnosic machine 'stamps' your vin into it aswell as your vehicle order (all relevant optional extras that your bike has fitted) all of this info is taken off of your bike at the time of programming and put onto the new control unit. You cannot put a used control unit onto any other bike for these reasons as it will cause conflicts within the bike so if you want to sell it privately the only person you can actually sell it to is the owner of the bike that the control unit is programmed to. BMW will not give you a refund for any control unit you order. If you would have let the dealer that was doing the diagnostics on the bike order the control unit and they misdiagnosed then the cost would be with them but as you went ahead and ordered it yourself, although they told you that was the problem, personally i think the cost should lie with you.
Admittedly the delaer should have diagnosed the problem correctly the first time but a broken wire can be sometimes hard to find, if it is literally just split then it could easily just sit together giving the appearance of a connected wire and any elemants could break the circuit like heating the bike up could adapt the loom just enough to break the circuit or turning the handlebars to on side.
OBD2 is not used on bikes. BMW use their own diagnosis bus which connects to thier and after market diagnosis systems. The system is far from perfect and does throw out the occasional control unit failed diagnosis, and it is far from just plugging it in and it will tell you what is wong with the bike, you actually have to do all measurements manually with a multimeter and then enter them onto the system for it to decide what is wrong. All it does is give you a guided diagnosis, a step by step guide of what wires could be the cause of the issue.
The can bus system contains only 2 wires, a signal and a confirmation, which basically allow the control units to recieve signals for switches, lights, sensors etc without having to run signal wires to each control unit that needs that signal e.g the wheel speed signal is sent to the abs unit only then the instrument cluster gets the speed signal from the abs unit though the can bus lines. It is actually very simple when you break it down.

Just as a final note, although you have found the problem now, i would have said that your problem was the wiring. Your bike is too late a model to be fitted with the faulty ews ariels, which all were replaced under recall anyway. Im guessing that the break probably would have been around your headstock, either at the bend in the wire or where it is cable tied to the frame, i have not had one break that hasnt been in either of those positions.