I'm so sorry for the delay in touching base, things have been crazy since the Skull mess.
Rumors are true, Hotch was indeed replaced by a clone and it took both me and Boy Wonder to unravel what happened. Cue nasty firefight in the office complete with injuries (worst was a bruised ankle and bruised ribs, 2 different people) and trashed gear (mostly my end: the box of parts from Radical Edward, Iceman and our guy in Wales got here just in time). So that should explain what's been going on in Team BAU.
I've been in touch with people both on and off the Network and I'm still stumped. FBI systems were targets of the Skull as well so security has been upped like mad on my end along with the team as a whole.