From what I understand, KyoAni have changed a lot of things from the light novels. Ruru and front tails, as well as some of the episodes seem to be 100% anime original. Considering the role Ruru had on the later episodes, a huge part of the ending was anime original, even though Enigma and that Rupa phantom seem to be the same character. And plot points from the LNs seem to have changed, like that device they got early in the season. It's basically not an adaptation anymore, as they take the setting and the characters and they mostly do their own stories.
Even if a S2 happens, I'll be surprised if they take the story from the second light novel. They still can present the story slightly changed, but it's apparent that they intended for the fanservice to be the main draw for the anime and I doubt they'll give this up in order to have an actual plot. They'll just add a few new characters and then they'll follow the same format as S1.