The novel is still unfinished but I'm halfway through it though. Anyway, now that you've mentioned it, my comic is not following everything in the novel. As what you've said, there are parts that is receiving changes because I feel it's much better if I do it like that. And I think it would be much interesting compared to the original version. I really tried to stick strictly to the novel, however, there is always that time where a brilliant idea comes in which would contradicts your planned path. When that happens, I will undergo a thorough analyzation whether it would create such drastic changes in the story or not. If the changes or effects is minor or none, I would completely change that certain part which I think is much better than the original one. But if the changes would greatly affect the course of the story, that is the time I would stick to the novel.
As you can see, the novel is following a strict timeline, what I mean about this is, if a certain character suddenly change course, the other characters will be affected since that person who altered his/her course will not meet a certain person or will not arrive in a certain place in time. And every events that should happen in his/her presence would all fall because he/she is late in that specific time. It's like "Chaos Theory".
In my case, I really review everything before changing a certain part so that it won't affect the flow of the story. This is one of the problems of a planned story because if you suddenly thought of an idea, greater than the planned one, you have to review every parts of the story that you think would be affected with the change.
But, honestly, I'm not facing any problems so far with the comic even if I change some parts of it. The Novel is 4 years old but if we add up the planning process, it's almost 7 years old now. Hehehe. This is also one of the perks of writing the plot first. I can say, my novel is currently not facing any conflicts because I've edited it numerous times to get it as flawless as possible.