If you are looking to add the additional reputation sometimes rewarded with a specific scenario, I have found this to be a two-step process. I first award fame, reputation, credits with my slotted faction and make sure that is credited fully, then I edit that journal and change the faction and add only reputation (and maybe additional credits from other sources). It will initially look like it is not crediting the specific faction but once I go all the way through it shows up correctly.
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