I must say I do not know the answer. However I have noticed that on a planet I modified the water level on, I have a similar issue with the water texture. Some areas are fine and others seem to be missing sections. I would be interested to see if these two things are related in some way.
Ah Yes! I've ran into this before as well as when water seems to be getting painted on and slowly rendering as one approaches the surface of the planet. I don't have a real solution but if you tweak the slope and elevation of your biomes and sub biomes you may eventually see this issue be resolved a bit. The temperate playfeild.yaml seems to be the most sensitive when raising and lowering water level.
The temporary ones are just loading errors, leave the area and come back, they fix themselves. The permanent ones are corrupted .raw files, I think
Besides switched it to and from creative I discovered another 'path' to the same problem. I started a game on Omicron with a random seed. But when I decided to go to Akua I wanted a specific seed from another game. So I modified the Temperate yaml and set the custom seed for Temperate (normally that custom seed yaml line is commented out). I then went to Akua and it loaded my modified Temperatebyaml with the custom seed. Then I returned to Omicron to find the same thing you reported. It appears that returning from Akua to Omicron the custom seed was cached and it used that seed in combination with my Omicron terrain modifications from digging to render the landscape. To fix it I got the original seed from starting the game then had to modify the Desert yaml with that seed and go back to a save on Akua. Then when I returned to Omicron the Desert yaml seed replaced the cached Akua seed and all was well.
Yup, changing seed is the cause. When going to creative, it tends to want to go to seed 0 at some point in the transition :/
