Is it theoretically possible to extract all ice and water from moons with subsurface oceans like Ganymede or Enceladus?
What would the consequences of isostatic rebounding be if this was done on a global scale?
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The answers to this question rely heavily on exactly how and how quickly you intend to remove all that water and ice. For the purposes of conversation and simplicity, I will consider the removal to be complete extraction without replacement of any kind, and two possible time scales, those being geological and sub-geological.
Geological time scales are often measured in the 100's to 1000's of millions of years. This is, of course, a huge time scale to consider, but probably realistic given the scope of removing that much material from a celestial body. Over that period of time, I think the transition would be relatively slow, in the sense that yes you would see expansion of the core and mantle, but probably at such a slow rate that nothing significant would happen to the planet. The thing to keep in mind, however, is that isostatic rebounding on Earth is due to the receding of ice sheets that were about 6 km thick or so. Ganymede's layer of oceans and ice sheets is estimated to be around 8oo km, or nearly 100 times thicker. Also, these layers cover the entire planet. Were they to be systematically removed, the moon would lose at least a third and maybe even half of its mass. If this were done slowly, I posit there would come a point in time when one or both of two things happens: 1) The core loses enough pressure and heat that it can longer maintain a magnetic field, and 2) the core undergoes phase change to solid. Obviously neither of these options are great for a celestial body, but the latter would be catastrophic, as a large amount of latent heat would escape into the body over time, causing general destabilization and at a point well before you had all of the water and ice collected, the moon might crumble.
In this scenario, we are effectively talking about millions of years or less. This rapid material removal would probably end in a similar fashion to the previous scenario, just more spectacularly so. If the core was able to depressurize at a high enough rate, you could probably get the object to shatter, more or less. I think the effect would be more pronounced if you were able to snap your fingers and it all be gone as opposed to mining it all in a hundred years or so, but I'm sure you get the point.
Basically, I wouldn't do it unless you really wanted to kill the moon and give its mother planet some shiny new rings or something like that. The scales and masses involved are large enough to lead to destruction in every direction.