I tried reloading the game from right after France's surrender in June and then tagging over to Bolivia (I don't know how to do observer mode).

What happens is that France starts to research the Focus to appeal to the colonies, but even before they are 1/3 of the way with Central Africa, all of West Africa defects from Vichy to Free France on August 28 1940?

I suspect that this is what also happens in the rest of the colonies in my game, yet I cannot find any event or Decision anywhere - neither in the Free France nor the Vichy France setup that gives any indication of how close a territory is to defecting?

I tried searching the Wiki, but it appears that La Resistance events such as the defection of territories have not been made into entries yet?

As far as this mod goes, it might be an outdated script from before the DLC that fixed a certain situation in Africa after France capitulated. This script only runs once when France capitulates and it transfers some African states to Free France. But it sounds like your issue occurs after the capitulation, so it's probably something else. I'm not familiar with how the border wars or defections in Africa work.