Alright, four things to get done in the security center:
1. Lock that sucker down. We're not the only ones with access to the Palace Cortex network at the moment, although that could possibly be changed.

If not, I want that sucker sealed off as best we can.
2. Gather intel. We need to know exactly what's standing between us and our exit, every inch of the way. As far as the neutron drones go, we might be able to detect them through other means, other cameras, power use, data flow, a fancy map, something.
3. Lock down our escape route. Close and seal every blast door between where we are now and the Black Gate, make a secure corridor so we don't get lost, don't get locked out and don't have to worry about nasty surprises any more than we already do.
4. Clean the escape route out. Fill that sucker with attack drones and sweep it clean. We're gonna be at least five minutes or so, that's plenty of time for as many drones as we can get our hands on to search and blast everything that looks like it might be threatening, and I mean everything. If the drones spot a suspicious-looking end table, I want it reduced to splinters. Neutron drones are the big fear, that's why I want everything that's not structural to the building in our escape route destroyed (and some things that are), if we can't detect them, we just destroy everything. Especially in the Repository vaults and in the Black Gate room, get at least a dozen more drones on that sucker and kill everything. After it's been swept, activate the killswitch on all the drones and blow them up, burn them out, whatever it does to take them offline in an emergency.
Edit: On #4, we'd probably need to create a sterile cordon around the sealed doors, say a hundred feet or so. We still kill every drone in the Palace once we're ready to roll out, though. It'll be the last thing we do before we crack the doors and leave.