Try to just delete all the spheres an box of the .zon (using s3d) and raise the armour, HP and crashdeep of the uboat.
But with this you will disable all the damage of the uboat I think. So, perhaps just raising the HP
and crashdeep could be the trick? Also in zones.cfg you can raise the floodingtime, hp for compartments and making flotability=1 for all compartments.
