Given that skyscrapers seem to describe buildings of 40+ floors, losing 3 is less than 10% of the total floors, possibly a little more of the total floor space given that upper floors may not have the same dimensions, offset by possibly fewer elevator shafts beyond certain points. If the bottom can be retrofitted to be very secure in water (extra concrete?), then I don't see why you would abandon it. It's not like you're constructing a whole new building and have to forego three floors, it's already existing and it's just a matter of putting the work in to make sure it's still usable.
These things are all anchored into bedrock anyway, so it's not like you should have to worry about the material under the foundations shifting or eroding.
These things are all anchored into bedrock anyway, so it's not like you should have to worry about the material under the foundations shifting or eroding.