First things first -- love the new Factorissimo. At first I didn't really like the new port layouts, but it just makes for a different kind of challenge.
Recently, I noticed that a couple of buildings had vanished. At first I thought I'd accidentally deconstructed one of them, but when I went into an adjacent factory built with the same blueprint, the same building was also missing. Weird.

I didn't think much of it, but as I was hunting around for my blueprint books, I noticed they were both empty, and all I could not find any blueprint sheets anywhere (blank or not).
I wish I had more info, and given that I'm running a couple of other mods, I can't even be sure if Factorissimo2 is at fault. But I thought I'd post it here anyway.

I've set factory buildings to unblueprintable in 2.0.3, which means that your blueprint items shouldn't place any more factory building ghosts, so are you sure the missing factory buildings were there in the first place?

Your blueprint books are probably empty because you sent them through a factory connection. Factory connections don't preserve item data because of performance reasons.