Well the 32gb really has nothing to do with the storage that stores the N900 internal workings. That partition is called eMMC if i recall right. So formatting the 32gb drive does nothing but clean it. It pops up after a format just like before. At least it did when i tested it.

Only thing i noticed was that the icon for the device when connected to the pc was gone. It was replaced with one of those genereal removeable disc icons found in windows.

But im 99% sure that a format of the 32gb storage will solve your problem