Issue seems to come from Any Planet Start's 1.1.14 update, reverting to 1.1.13 fixed it for me. Something to do with changing where/how they handle planet tech hiding.
local utils = require("utils") --[[@as APS.utils]]
local planet_technology = APS.planets[planet].technology
if planet_technology then
utils.remove_tech(planet_technology, true, false)
end
Is the bit of code that was added to data-final-fixes.