I wouldn't put money on them being accepted for license issue. License in your hand is a different situation.
They are making it up as they go along. Nothing in the EU regulations was written with a member being able to escape in mind.
Also as well come the day there is going to be loads of very pissed off people scurrying around trying to figure out what the hell to do. A wannbies exams is going to be very low down on their list when the summer season is destroyed for tourists in the med. To be honest this not being sorted now is going to cause huge issues in that respect what ever happens.
Flights from and too the UK are very profitable and are what keep more than a few operators out of bankruptcy.
I would put maximum effort into getting them passed ASAP and your CPL in your hand. After that its just a valid date in your license records.
I don't have a clue what to recommend in relation to when to do the IR, Mty gut instinct is that as soon as the day passes and no deal is done then they might sort something sensible out. If they don't and start on another round of call my bluff I suspect it will be worth delaying getting the IR.