For Abyss of Hyperscape, the manga is an adaptation of the movie.
Wikipedia mentioned about this in a brief,
A manga adaptation of the film illustrated by Chibimaru began serialization in Media Factory's Monthly Comic Alive from February 2014.
However, the confusion between the continuity between the manga and the anime might arise because the anime overtook the original source (light novel)'s progress.
From Japanese Wikipedia,
Since the anime's production planning was about to start when the 3rd volume of the original source (light novel) had only a summary, episode 1-18 would be based on volume 1-3, and episode 19 and later would be anime original story based on the present time chronologically. However, while the broadcast was planned to start in the second-half of 2011, it was delayed until 2012. Because of the time allowance, the production for the whole 26 episodes has finished before episode 1 was broadcast. Moreover, the time allowance made it possible for the production to contribute to the different plot development and experiments. The "space opera" feeling from the original source was reduced, and alien-like races were not introduced. However, regarding the oldest pirate being alive and more, some plot from the original source still remained, but also some of the settings from the anime got adapted into the light novel too.
- The light novel was adapted into a manga, and partially into an anime.
- The anime continued with an original story while the light novel was still in progress.
- The movie continued the anime, and a new manga adapted it.