This may seem to be a weird question, as you wrote a lot of side stories that seem sort of random (many of which are my favorite Bionicle stories). But, most of those stories either explain something from that or previous years (like the Mutran Chronicles) or have a thematic connection to that years story (ie, Birth of a Dark Hunter in 2005, The Kingdom in 2008). The story itself doesn’t really explain anything new about Lihkan of Nidhiki, Tuyett is dead next we see her, and the Nui Stone plot thread ends quite abruptly. The most thematic relevance it has to 2007 is… water = bad, I guess. Was the story created just to have an object for Makuta to seek in Into the Darkness and provide the back and forth between him and Matoro, or to set up Tuyett to be the villain in Dark Mirror (and, for that matter, did you plan that far ahead)? Or, did you just want a Bionicle murder mystery?
I rarely set the side stories up to tie into main story. In a lot of cases, they were written as a way to explore the fact that BIONICLE could work with multiple genres, not just action-adventure, or because I wanted to play for a while with certain characters.