So at this point (TMA 31) we know directly from Jonathan that he is staying at the Archives more; we can assume he would sometimes spent the night without going back home.
Martin already sleeps there.
I’ll assume that if others (Tim, Sasha) would also spend more time at the archives it would have been a point worth making in this situation since Jonathan tries to underline the fact that they are being hunted.
Which means it’s just the two of them. He and Martin spent more time together. Which is why I believe we don’t hear Jon picking at Martin anymore. Especially as he probably first hand sees him doing the research more then he would if they only saw each other during office hours - Couse you can’t tell me that they weren’t working extra hours late into the night; probably also keeping each other company by working in the same room (after others left) simply for the comfort. He sees how Martin relentlessly checks every information twice, thrice usually even more times - because in Martin’s head he has to. Jon sees how the way he was undermining Martin’s research got to the man. Even if he doesn’t know why. Even if he doesn’t know yet that the reason is the way Martin’s mother always dismissed him too.
We always claim that Jonathan felt remorse firstly later - but I think he already did back then; just didn’t deal with it himself yet. But we see the seeds of it in the way he starts to respect Martin’s findings. It’s in the way he doesn’t make snarky comments at Martin anymore, sure. But also he doesn’t question if more could have been done. He takes it at the face value. It’s even in the fact that he lets Martin join forces with Tim who he already trusts - or if they done so in the past he now starts to acknowledge Martin’s part in investigation (which also makes you wonder how many times before he didn’t).
And so as they “are stuck” they sometimes talk. We are humans it’s in our nature that we socialise after all; so simply by proximity they get to know each other better, find out each other’s preferences. Jon ends up warming to his new assistant as he gets to know him better; Martin falls for him even more - if we assume (which for the sake of this I do) he already had a crush on Sims.
From both of them Jon is obviously the less paranoid one still holding onto not supernatural explanation with his dear life - as admitting that explanation is in fact supernatural would mean that they enter uncharted territory and are actually helpless without any real knowledge whatsoever. Even by the very end of TMA 32 he still can’t deal with the idea of Jane Prentiss not being completely natural. But also completely terrified of feeling watched.
But they move on, they live on ‘couse there is nothing else to do than look into it as any other statement. But I believe it was detrimental to Jon’s belief in The Fears and at that point he already did believe far deeper than I think we assume. Just couldn’t admit it. Since admitting it would mean not knowing what to do, how to even start fighting it. It would also allow him to be Seen.
And the reason he feels after this statement? It had to be coming from the fact that Jane Prentiss told him exactly who’s he about to become. Who he already became as soon as he recorded the first statement. A resource to store information instead of one of a help. So he acknowledges it, but still dismisses the mere idea of this or other statements being unexplainable by “natural” things. Still dismisses the statement from fear of being Watched that I assume absolutely was boiling him from inside out at this point of recording.
And Martin was there in the Archives the entire time looking at Jonathan’s change. The others did too of course. But there is always something more intimate when you’re in only each others company and not in a group. I’ll assume he noticed the shift in Jonathan stronger and more detailed than others.
