That would be my assumption as well. Of course, that's all it is... an assumption. I suppose that someone with some foresight could have secreted it away before the fire occured and destroyed just about everything. And, if Frankenstein's diary survived the ordeal, then I'm sure that some scriptwriter could have come up with a way for the monster's original, discarded brain to have survived as well. But, since that's an avenue they never bothered to explore, I'm going to stick to 'Destroyed in the fire at the climax of GHOST OF FRANKENSTEIN.'
I do think it would make a great movie if the original brain was saved and another operation was performed to reunite the brain with the body. If only we had a time machine---it would be cool if in said movie, Karloff took back the role of the Monster. Oh well.