Finningley Boy, you are a little behind the times. The Boulmer Interim Facility closed as a CRC in the early 90s,though the buildings were re-used for a bit by No 1 ACC. The bunker at Boulmer has subsequently been the home to CRCs using first the ICCS* then UCCS** and now UCCS2*** (or CERBERUS). The second CRC in current use is at Scampton in an above ground facility (in the building where the Damn Busters Raid was briefed); this also operates as No 1 ACC.
Back to the original question, Boulmer is now the only underground facility operated solely as an AD facility (although the National Air Defence Operations Centre operates out of the RAF High Wycombe Bunker).
When the decision was taken to close Neatishead in 2002(?), the common line stated was that in the event of a resurgent Russia, the UK would have 10 years to return to underground operations. What no-one has ever explained is how we know when the 10 years starts - Russia taken over by an unchallenged President who builds a power base to the extent that he is able to change the constitution so that he can remain in power in perpetuity, then invades a candidate member of NATO and starts throwing his weight around in the Middle East? Well those of us being taceval'd during the Cold War will recall scenarios that started a bit like that, but which many considered far-fetched.
As far as basing is concerned, few places are safe. I would put money on Waddington, Wyton, Lossiemouth, Brize Norton and High Wycombe staying - for obvious reasons. I have no ability whatsoever to influence the decision-making - this is a rumour network after all. I await developments with the same interest (and frustration) as many others in (and outside of) the Service.
STH
*ICCS - Improved United Kingdom Air Defence Ground Environment Command and Control System (Built by UK Systems Limited).
**UCCS - UK Command and Control System (Built by IBM).
***UCCS2 - UCCS 2015/16 tech refresh (Project CERBERUS) (Built by IBM).