Harmonized colonists that are moved to a planet without a Machine Altar will always become Disconnected. If they're not Tinkers, this means they will revolt; they become horrified when they realize what's been done to them. I don't recall whether the presence of ground units can prevent this through Martial Law.
Unfortunately, with a Colony Base I don't think there's any way to override which colonist is selected, which will be whatever the majority non-Primitive population is on the building planet. So in general you don't want to build a Colony Base from a planet that's not majority Tinkers.
If you have tanks on the planet that built the Colony Base, you can try moving one to the new colony on the turn it's created to see if it prevents the revolt. Or you can rush-buy a Machine Altar.