I don't know if they had that planned so far in advance. It's possible but here's some things I know first hand.
I was at Bethel living in 107 (or Ghetto 7 as we called it) in 2003. That year they started moving people out of the building floor by floor. The reason was so they could do said renovations. A couple years later they installed new laundry facilities in one of the factory buildings because shortly after that 360 Furman closed up so they needed a new laundry.
There was probably a bit of future proofing involved in renovating 107, since it could easily be flipped for residential living. I don't think they would have put all that money into the factory complex at that point if they planned on closing up shop in Brooklyn, even if it was 10+ years later. I don't think they have that sort of foresight.
I still have no idea why they bought land at Warwick. There is TONS of unused land at Patterson and Wallkill. They could have economized even further by building a new HQ building at Patterson, for example, since some of the departments were split between Patterson and Brooklyn.
I think they were expecting to be rolling in dough so they went ahead with the plans. They totally didn't see the financial issues they are experiencing.