On the whole, I tend to weigh actual cutscenes and dialogue over Sebastian's journals. The problem with Sebastian's journals is that they were written by him. They're clouded by his own personal bias, and if you'll notice, he spins things in his journals to make it seem like everything he does is justified and he's always right. The tone that he writes in is very level-headed and confident, and everything he says sounds reasonable to us because it is reasonable to him.
So, there's that, but there's a problem with The Consequence flashbacks, too -- namely, we don't know where the hell they come from. At least with the flashbacks concerning Jimenez, Ruvik, and The Administrator, we know the source -- it's Ruvik, because either he was there at the time or he dug around in The Admin's skull and pulled it out, since we know that Ruvik marked him "long ago." But in the KCPD flashbacks, I don't know whose memories Ruvik is pulling on, and we only have two choices.
The only thing we can really do is take all of the statements about that time period and lay them on top of one another and see which ones corroborate a story and which ones contradict them. Let's use Sebastian's mental breakdown as an example. In chapter 6, Sebastian says, "It never affected my work." In context, "it" is referring to his drinking and his general mental state after the fire. Now, is this statement true?
We have two pieces of evidence that corroborate his claim. The first is in his journals (big surprise), where he says that he only drinks at home and it's his business and no one else's. We can't use this as evidence, because you can't use the same character's perspective in order to prove or disprove their claim. Of course he's going to back up his own claim that it never affected his work. The other piece of evidence is still in his journals, but it wasn't an entry written by him, so we CAN use it as evidence. In the IA transcript, Sebastian says that the KCPD can't prove a damn thing concerning any misconduct on his part, and they admit it. So, on the surface, it looks like his work really wasn't affected, because IA couldn't pull up any proof that it was, and they conducted a full-blown investigation on it. If that was the only evidence we had, then you could make a case for Sebastian being self-aware and say that his perspective AND his journals are both reliable sources of information.
However, we have more evidence contradicting Sebastian's chapter 6 claim than we do to corroborate it. Now, even though IA had no concrete proof, they knew that his drinking was a problem. They say so later on in the transcript. Even in Sebastian's own journals, he talks about how everyone around the KCPD thinks that Myra simply just left him because of his drinking. In the flashback in The Consequence, Joseph tells him that he's getting out of control. We can very clearly see that his office is a mess, he can't focus on his work, and he even baselessly accuses Joseph of hiding things from him. That looks an awful lot like this whole thing affecting his work to me. In that same room, we find one of Kidman's personal files, in which she describes Sebastian as, "Seems drunk half the time, but at least he's considerate. Is he really the one everyone's so worried about? He seems almost harmless." Kidman's perspective corroborates the flashback. And probably the biggest piece of evidence we have is Joseph himself -- Sebastian's partner who had to fucking work with the guy every single day and would notice immediately if he suddenly wasn't performing at his normal level.
Now, what's interesting here in this whole thing is that Joseph reports him to IA and not HR. If this was just about Sebastian's drinking habits and his clear symptoms of PTSD, then HR would be the place to go for that to make sure that he got the emotional and mental help he needed. But... Joseph goes to IA instead. IA is the place you go when you feel that another officer is corrupt or abusing his power or engaging in some other fucking super illegal shit. Which Sebastian super was. Sebastian's mental state was what led him into this illegal investigation in the first place -- one that Joseph probably thought would get him killed. Hence, IA and not HR. That is a huge difference, because HR would just put Sebastian on sabbatical and force him into therapy. IA could get him fired and possibly jailed for what he was doing. And for someone who cares about Sebastian as much as Joseph seems to? That's a drastic fucking measure.
So, is Sebastian's claim that his drinking never affected his work true? No. Sebastian is an extremely unreliable narrator for more reasons than one, and I would be hesitant to take anything he says at face value. His memories are scattered and repressed from STEM's influence, and he's quite frankly a person who is constantly lying to himself in order to just get through the day. He's a paranoid conspiracy theorist with a drinking problem -- and even though his conspiracy theories turned out to be 100% real, we still need to recognize that this is a man who operates solely on confirmation bias and who thinks he's never wrong.
So, to bring this back around to the original point, to a certain extent we can disprove the validity of Sebastian's journals -- but only to a certain extent. We can only disprove the things that we have evidence to disprove. Kidman's statements on Sebastian and Joseph confirm that those flashbacks have some merit, and they cast doubt on Sebastian's view of himself and his perspective of the world. Sebastian has an extremely romanticized view of his own marriage and of his wife... but we know that his wife has been working for Mobius for months at least and that she was the very person who recruited Kidman into Mobius and stuck her under Sebastian's wing in the KCPD. It's hard to imagine her as being this warm, affectionate, loving mother of the year all years.
If we look at the whole maternity leave thing, basically all we have to go on is Sebastian's journals vs the flashback in The Consequence. It's far more likely that Sebastian is straight up pulling bullshit out of his ass in his journals than it is that the flashback is incorrect -- because it's not just Joseph who mentions that she barely took maternity leave; Seb complains that she's never home, too. So, either he just straight up fucking lied in his journals to make himself feel better about his household situation even though he knows the truth and remembers it quite well (which is always possible), or he doesn't want to acknowledge the truth and is still lying to himself about it and those flashbacks were actually pulled from Joseph's head, since Sebastian's memories can't be trusted (which is also possible).
I think that there's enough reason to call bullshit on a lot of what Sebastian writes in his journals, but there are certain things that I don't think he would get wrong, like the day he was promoted or his wedding date or his daughter's birth or Myra's disappearance. To some extent, we can take his journals as a nice timeline for reference, but the actual events in and of themselves are completely skewed and tinted by his unreliable bias. I guess you're right in saying that I can't prove one way or the other whether he was keeping the journals in real-time or not, but I'd say that the one thing I think we can fall back on is Tatiana saying: "Memories are vague things indeed. It can be easy, at times, for memories to become distorted by others. That is why they must be cherished."
Now, that line in and of itself could probably fill out its own entire essay, because there's so much to be said about Sebastian's memory and his trip through STEM, but with regards to his journals... I don't know. Maybe I'm just floundering and searching for any kind of a starting point, because I've been having so much trouble just organizing my thoughts on this damn canon. Everything is so intertwined and it's so hard for me to break it up into sections or form a coherent thought on it, because it's like a goddamn spiderweb.