Hydrosia

The mine-able rocks don't reset so I can only mine them once. Is that intentional? I haven't gotten the odd keystone yet, and I'm certain that I've mined them all so far. Is there anything that I can do so I can mine them again?

When you go down, you should find a platform with a kyogre-like symbol, similar to the Groudon one in the Garufa Ruins. There should be a stone slab near it that you can interact with. IIRC, when you do so, it will ask if you want to stand in the center of the symbol. When you do, you'll face Kyogre. Beating it will save Amber.