I think I mentioned that before, but each chapter is first of all meant to progress the main story, while everything else is kind of built around it.
So, how do I plan them exactly? Well, it's more of a workload issue. As I don't want to release the update every half a year(or even longer), I try to restrain myself to certain size limitations. For example, initially Chapter III was meant to be made of 9 scenes, but after writing the scenario and planning everything out, I had to "cut" the size down to 7. The update is still going to be larger than initial release mind you. Also, the "cut" content was simply moved to Chapter IV and no, it won't affect the narrative as I'm planning most of the plot far ahead.
One thing is certain, if during the planning period I've said that particular event will take place on upcoming chapter, it will be there no matter what.
That got convoluted

. I hope I answered your question.
The first plan was posted back in late march, here:
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Gonna post one more up-to-date soon.