Hickory: Now, in BG1 there are flags that set those weapons as silver (and some as cold iron). These flags are simply not used in the BG2 engine
This is not true, those flag can be set and used in the BG2 engine. As a matter of fact, the greater wolfwere requires silver weapons in both Tutu and BG:EE, but not on BGT (this is by design and not because it is impossible).
Pangaea666: I think this must have been changed in later versions of BGT. I fought this beast yesterday. Was amazed at how quickly he regenerated. Had him at Near Death and Badly Injured several times, and suddenly he was Uninjured or Barely Injured. However, we hit him with much else than just the silver weapons. I spawned some ogres with a wand, and I saw they hit him with ~30 damage multiple times during the fight. At some point I equipped our tank Kagain with the dagger we found somewhere, but I'm sure he hit him before too, with a +2 weapon. What finally did him in was when we all could focus on him (all others dead), and Imoen and Kivan hit him with +2 arrows, and some of the previous acid strikes (spell) helped too, plus Viconia with a +2 hammer, and yet more Magic Missile salvos.
Epic fight, but it looks like +2 weapons can deal damage to him in today's BGT.
The greater wolfwere behaves differently in the different versions of the game:
In BG1 vanilla and BG:EE it requires silver weapons and regenerates 5 HP per second.
In Tutu it requires silver weapons and regenerates 2 HP per second.
In BGT it requires just plain magical weapons and regenerates 6 HP per second.