To prevent and/or dealing with Drone riots, or in this case, base facilities disappearing, try to make sure at each base:
There is enough growth (35 or better).
Influence the population to grow by providing Nutrients.
Provide living quarters for the population to grow and expand.
Assign jobs for each worker to take advantage of the bonus they provide for your base (Economy, Psych & Labs).
Just right-click to choose a job for each worker.
Provide security for your population inside each base. Sometimes, Drone riots occur when there are no troops inside the garrison.
Following this sequence each turn should keep the Drone riots down to a minimum and prevent base facilities from being abandoned.
Living quarters is the last thing you want when your having trouble with morale! Population cap is your friend that gives you time to get better organized before expanding the population further.
Watch your government types.... i think democracy is pretty much unusable if i remember correctly? anyway, allot of the government types MOOT themselves with over the top negatives... it is a bit frustrating.