When setting up a mission with an Independent force as the primary opposition, it would appear that their objective status (and/or units) are completely ignored by attacking forces. Is this the expected behaviour?
In the test mission I threw together; BLU (Invasion) vs IND (Occupation) resulted in objectives in BLU's TAOR are Reserved, with Reserve orders issued to every objective in IND's TAOR. No attack or defend orders are ever given by BLU's OPCOM. Left to their own devices, BLU's OPCOM will issue no other orders beyond this initial set-up phase and objectives within IND's TAOR will slowly become unassigned as BLU units are sent piecemeal to capture "unoccupied" objectives. IND's OPCOM on the other hand, issues orders normally at all times.
The above appears to be true in all possible scenarios vs an IND OPCOM. BLU/OPF OPCOMs never seem aware of IND units, though they will fight one another as determined by IND's hostility settings.