OK, I've got one: do we have any reason, other than secondhand sources which lead to "I heard ____", to think that ZUN changed stuff for the Windows games because Amusement Makers owns the copyright on the PC-98 games?
No, but others continue to believe it. Personally, I think it's hogwash, and there is no copyright conflict, bad blood, or anything of the sort. There are admittedly
some reasons to think that could be the case, but otherwise, just no.
First, AM is "just" a university hobby circle. Not an actual company, like I've seen some say when repeating the PC-98 copyright argument. Even if there was copyright, would anyone actually care to enforce or make an issue of it? Second, he used Mima on one of his album covers. So, it's not that he can't use her, he just doesn't want to. Third, he participated in Seihou, which if I have my timing right, he already graduated by that time, at least during the second game. It could always just be a senpai's favor, though. Fourth, he used some of AM's resources when making EoSD, which would be after Seihou 2. Still, neither of which would seem to say he was on the outs, or in conflict, or anything.
However, like I said, it doesn't mean a copyright doesn't exist. It could, and I've seen some say that this is why ZUN is so touchy about copyright these days. Because he possibly came upon copyright problems during the making of EoSD or PCB and it was since then that his stance changed. I've also seen the number of supposed expy characters around this time mentioned as an argument in favor. This theory says he couldn't use Shinki, Yumeko, or Yuuka, so he made Remilia, Sakuya, and Yukari, or changed Alice/Yuuka enough that they couldn't be called the same character. It's clearly all speculation and no fact, and some of it a stretch, but who knows.
In the end, though, I think ZUN is just the type that doesn't like to look back. He may think of PC-98 as being particularly unrefined and most of all, doesn't want to dredge up old creations and try to awkwardly fit them into current Touhou, when he'd much rather make new ones. Especially not 10-15+ years after the fact now, when the chance or any desire to has passed, or when there are some that clearly wouldn't fit. You know, the actual reason ZUN has said as to why he hasn't included many old characters.