Still exists in vanilla. It's fixed by saving/reloading your game.Vanilla have fixed the bug where you still suffer from malaria/severe malaria if you researched the tech after the colony is already started. The mod still have this bug.
Unrelated note: I'm torn on the combat changes here in the mod. On the one hand, the vanilla combat mechanics are -terrible-
On the other hand, the current mechanics as implemented favor zombie hordes way too much. China is an unstoppable monster with the combat changes in the mod and you really can't play anywhere in Asia right now with how broken they are, they just end up steam rolling everything. I think more tweaks are needed here- perhaps doubling the effectiveness of all the tech increases and also folding in the gun production mod, which adds combat effectiveness to your armies depending on what gun production methods you are using. This would allow armies to use full frontage in combat but make tech still matter.