I think I know what you're talking about. I bought a Nashbar branded ISIS bb once, the left side "cup" was pressed over the body of the bb, maybe to assure that the parts didn't get separated during shipping, I don't know. Anyway, if I remember correctly, I was able to twist, turn, and wrestle it off by hand. Beyond that, maybe carefully secure it in a vice, making sure not to damage it, and then twist, turn, and wrestle the parts apart-
you are trying to remove the side without the flange, correct? sometimes you have to persuade it a little bit by LIGHTLY clamping the cup in a vise (protecting the delicate threads with a rag, or blocks of wood, or using soft jaws, or a shaft clamp of the correct size) and then giving the spindle a tap with a light weight plastic or rubber ended mallet.