With two separate VC's in separate vlans they operate completely independant from each other -- ARM on one VC group is independant of ARM on the other VC group.
You might considder updating the SW as your first step. Earlier 4.0.0.x seemed to have a lot of random issues similar to this (sorry, I don't have specifics) and they seemed to clear up when upgrading to v. 4.0.0.7. v.4.1.0.1 is the latest release; HOWEVER, there are a number of limitations imposed on the IAP-9x with 4.1 so be sure the read the Release Notes carefully to see if they apply to your network.
Also, is the outage only being reported in AirWave? Is the network actually up or down? What version of AirWave are you running? 8.0.3 is the current release, 8.0.3.1 will be out in the next day or so with fixes for some VisualRF issues, and 8.0.4 will be out in a couple of weeks with IGC for IAP 4.1.