Flurry Of Blows Problems
Mixing Unchained Monk with levels of a class that is "functionally" like a monk class, including their version of the flurry seems to be glitched. The most easy combination seems to be mixing not with brawler (which has its own, different flurry of blows). but the "Sacred Fist" archetype for the warpriest. (Advanced class guide)
This seems to create glitches in the flurry of blows, i either end up seeing the flurry suddenly improve dramatically the moment i take the unchained monk level... or i end up seeing negative numbers and other weird stuff whenever i take a level in another class that gives that class the flurry of blows... of the "normal monk".
Problem is... the unchained monk and the "normal monk" classes were never meant to be mixed.
So i don't know if i'm breaking the rules or not... because let's face it. Nowhere it says "do not mix" it's just evident that they are incompatible. So if somewhere they said that they should effectively never mix.... yeah i'd like to know so i can be at peace.
If i were to take a stance i would keep both flurries, present them clearly and distinct in the character sheet and let the player's GM decide which one the player is allowed to use.
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What i’m proposing here is to consider those classes as using normal monk rules, and if one takes an unchained monk at some point either switch to the unchained monk ruleset or present both rules independently from each other and let the GM sort it out. It’s the only way to solve this bug that i see. This will most definitively need to be done on the data by either dividing the two flurry computations but have them both take in account the total monk levels
PCGen teams cannot make rules determination for Paizo. And that is what your report is looking to be. I cannot give you official clarity. I take what the publisher says, and implement it.
Most everything is geared towards the normal classes, including Archetypes. If you mix UNCHAINED w/ non-unchained Classes & Archetypes, you’re going to break things. I cannot hope to program every corner case when we want to make the program as open for all the legal classes.
I also cannot program in two different Flurry of Blows, it will conflict. The code of both class features change the code of the same object called UDAM (Unarmed Damage). You want that, then ask the code team when the Damage Dice and Compound support will be implemented for the replacement formula system.
Currently I cannot see an actual bug report here, other than a vague “Hey mixing two invalid class features causes problems”.
I recommend you open a FAQ/Ruling post over on the Paizo forums, and see what they say. When you have your answer, share it with us so we can either address the problem with a publisher legal solution, or at least know what we need to do in the future.