Soul means ghost. When the ghost flies over the dead body he formerly inhabited you can zap the wand of resurrection, otherwise, you can't.
As for certain level features being disturbed, that means, for example, killing/discovering certain level specific unique features, and then dying on that level, will prevent you from discovering that body on that level in the future.
Yes, Cap, permanent, I think we may have just covered it on JConserv but it was in fact determined that once the duration of an effect reaches a certain number, it rolls back over and will not ever wear out.