Yes. According to rules section 1.4.1:
Important: A player Faction while executing an Operation, Special Activity, or Event may remove its own pieces to Available Forces. EXAMPLE: Insurgents without Available Guerrillas could remove Guerrillas during a Rally (3.3.1) in order to place them Underground.
This means you may, while executing a Rally Op (or whatever) choose to pull bases back to Available, and then place them normally. The COIN titles later in the series restrict this ability somewhat, but it is allowed pretty liberally in AA.