SaverLoader (saver_loader.gd) can save procedural scene trees of arbitrary structure and rebuild them on load. It persists data from procedural and non-procedural objects – but only what you tell it to persist! Saves and loads are very fast because we don't save whole objects.
This system is used in I, Voyager to save/load a procedurally built Solar System with >100 planets & moons and ~65,000 asteroids. Our save/load times with an ssd drive are on the order of ~1 second!
For a detailed how-to-guide, and to get help or give feedback, please see post in either:
Current version is 1.1 (saver_loader.gd from I, Voyager version 0.0.5).