There is a timeline. At some point after the Dominion War and probably shortly after Voyager gets home some event occurs which splits this timeline into two distinct timelines. One of these timelines is the one the vast majority of the post Voyager novels occur in and one is the timeline Star Trek Online occurs in.
No, that doesn't work. As I've pointed out before, there are alien races in STO that are portrayed incompatibly to the way the novels portray them. They can't be divergent timelines that share a common history. They're just different licensees' speculative extrapolations beyond canon, and no attempt has been made to reconcile them with each other, even though STO has borrowed
some ideas from the novels while disregarding others.