I suppose it's already late, but anyhow:
The problem stems from the governance type. Any change is incompatible with AoTD and the water shortages will occur. I've delve into both IndEvo and AoTD VoK mods and I haven't found a way to make it work.
The easier solution is rebuilding the planet with console commands without the governance type change.
Firstly take everything out from storage. Then, console commands destroycolony. The planet conditions will be maintained. You can add all thi industries and structures with the addindustry command, in case of doubt, list industries. For the population, add condition population_x where x is your planet population. For the items spent in recolonizing, additem crew 1000, additem heavy_machinery 400, additem supply 200.
You'll have the same planet with the vanilla governance. I hope someone can take a deeper look and find a better solution through code.
By the way, centralization bureau won't work with AoTD industries, so you should include them in the IndEvo whitelist CSV, using the IDs found in list industries.