I've been trying to find what the hell is going on with my Vodyani games in end game where all of a sudden my empire which is mostly at 80-100% happiness save for a few systems is going into anarchy and change from democracy (for those extra representative) back to a republic with some random faction in charge (Scientist). I say random because of the fact that when a democracy is selected, scientists are barely a blip, it has been Religious, Militarist/Pacifist and Industrialist. 

Even with the Bob Act (less dust/more happiness per population) those systems just aren't going anywhere near content (and unfortunately didn't have any sources of grapevine to have an income to make it viable to add to system upgrades).

While the solution isn't terrible, it's not great either (no extra bonuses from being happy). The only way to stop it has been to pass the sinners and saints bill to force all my systems to 50% content. I've also seen some solutions of changing the xml file for governments, but since two years ago that file has also changed and the terminology doesn't match up. So how would I go about fixing this so I don't have to use this particular method of keeping people content (also built every happiness system improvement and it hasn't helped)

Why do you choose democracy anyway? You could just stay as a Federation, buy 10 heroes and get an easy conquest victory. Or switch to republic an enact saints and sinners for happy approval. 

About whats happening, you probably have a couple systems with very low approval, this start a rebellion timer after which your government will switch. This happens to me quite regularly when I am playing Horatio and have not yet swapped from dictatorship to Federation and are about 7 systems above colonization limit. The easy solution is to just keep using manpower on each system (costs about 20 so its basically free) to stall the timer. However this will lower your food output aswell, so you have to be careful to not starve your pops. 

Upgrading Arks to a higher system level also increase approval, since you cannot terraform.