The missing chapters were all done by the same group (Spruce Tree Scanlations), so that group must have asked to have them taken down. They can still be found on other sites.
And speaking of missing stuff, one Takano Saku series that hasn't made its way to Dynasty yet is The Vampire's Bride -- which is, among other things, a partial sequel to this one! It's a combat yuri series a bit like Valkyrie Drive, but the pairs are vampire/human, and instead of one turning into a weapon, the human is a juice box to power the vampire. The main pair seems to be visually based on the characters of Mermaid Lovers, but there are two other teams who get the spotlight in chapters 2 and 3, and those two are obviously just the couples from Vampire x Junior.
The most interesting part is that when Gouma-den was finishing up this series, the first chapter of The Vampire's Bride was already out -- and while they didn't mention it, they definitely knew about it, 'cause that's where their credit page pic was from!