Considering all the stuff that is mentioned and the theories that have been thrown around before, I think having some stuff missing from replays might be intentional? Or maybe he is just bad at it idfk.
It's definitely intentional, but it's also an asshole thing to do when it just makes people jump through more hoops to see something that they've already seen before. He clearly likes laying out all this foreshadowing and symbology so that people can make predictions about where the story is going to go, so I don't understand why he thinks it's a good idea to obfuscate things retroactively.
He's definitely an ass/bad game designer.
I understand (don't like it, but I get it) that you can make your game difficult to understand, by using hexadecimals and ciphers, and hidden meanings, and flashing pictures, that's all fine. Annoying on a replay because you have to keep looking for all its meanings again - but fine. It's part of the mystery thing and you as a player having to decipher everything. Having a replay feature is the mechanism by which you engage your players in this discussion even more, since they can rewatch everything and take screenshots and discuss it. All of this works together as a strategy for how to engage people (if it's a good strategy or not is debatable).
However, cutting off parts of the events on replay runs counter to everything I just said. It's just dumb. How can people decipher stuff if they have to replay 2 full weeks of content to even get back to a random 3 minute dialogue? (or sometimes even just one sentence?) It's just idiotic. There's a difference between: the code being right there and you having to work on it to translate it, and him punishing you for not having saves from each single event on the offchance it might have been cut off on replay.
Stuff like Sensei's mother's name being cut out in replays, while, in game, it is implied to be something we aren't supposed to see, could explain why.
Same with the Shapeshifter/Himawari. Like she's pointed out, memories of her aren't supposed to stick:
Lorewise, the replays not showing certain things make some sense. Like how Sensei blocks out things that make him feel things he doesn't want to feel.
Why only (without URM) certain variables are replayable even when events that they cause one to miss, are also replayable, is a little immersion breaking though. I suppose The Shapeshifter requires fingering Ami and fucking Sara so that could be why the Replays ignore those variables when possible.
Overall: I can see why it's like this. Still sucks.
Also may be a way to gaslight players into thinking certain things as well. Over time, people forget or replace things in their memories. Replays could be a way to manipulate the player into forgetting or thinking certain things. Albeit, I'm probably getting into conspiracy territory.
