I can edit the milestoneSet file and one of the conversations to show you how it's done.
There's a caveat with branching the FP. RIght now the sequence of the milestones goes:
Start - Mission 1 - Talk 1 - M2 - T2 - M3 - T3 - M4 - T4 - M5 - T5 - M6 - T6 - End
When you add a decision and create a branch, the milestones start as usual until the decision between A/B:
Start - Mission 1 - Talk 1 - M2 - T2
But when the player chooses you need to recreate the entire branches (A/B) on the milestoneSet file:
M3(A) - T3(A) - M4(A) - T4(A) - M5(A) - T5(A) - M6(A) - T6(A) - End A (all missions)
M4(B) - T4(B) - M5(B) - T5(B) - M6(A) - T6(B) - End B (less the Defend mission)
The issue here is that you might need to have different versions of the same contract/conversation for each branch. If the player skips the base defense misssion, then any of the following contracts/conversations can't have any reference to that mission.
And everytime there's an additional decision, that creates more different endings that require their own milestoneSet branches. Add the decision at the beginning to skip the FP then you need:
Common: Start
Branch A: End A (Skip Flashpoint)
Branch B: Mission 1 - Talk 1 - M2 - T2
Branch BC: M3(C) - T3(C) - M4(C) - T4(C) - M5(C) - T5(C) - M6(C) - T6(C) - End BC (all missions)
Branch BD: M4(D) - T4(D) - M5(D) - T5(D) - M6(D) - T6(D) - End BD (less the Defend mission)
It's normal to have typos/grammar errors even when you're a professional writer. That's why editing and proof reading exists
I haven't played the final mission (will do later) but looking at the custom itemCollection the reward seems correct.
I couldn't find in the milestoneSet .json file any reference to adding a flashpoint complete tag at the end.