A character from Time's Enemy reappeared in DTI: Watching the Clock, and its events were alluded to therein. The Furies were referenced in SCE: Ring Around the Sky.
I've only got a vague understanding of how time travel is supposed to work in the modern Trek Lit-verse, but could it be that the MU did not diverge from the main reality until some point after the war between the Furies and Unclean, and the Furies' banishment to the Delta Quadrant? The Defiant could still have come back in time, but from an alternate/possible future.
Characters can exist in multiple timelines, so I have no problem with the idea that Heather Peterson has a counterpart. I did not know they were referenced in SCE, though.
^What's wrong with the idea of Invasion taking place in the Litverse? The Final Fury has some major continuity issues with the previous books in the miniseries as well as with VGR as a whole, so I count it as apocryphal, but I don't see any major problems with the other three parts. (Actually for a while I did consider Time's Enemy apocryphal due to temporal-mechanics credibility issues, despite it being my favorite part of the miniseries by far, but when researching Watching the Clock I realized I could make sense of its temporal physics after all.)
The main issue with the rest of the miniseries is that it takes a very different approach to the idea of the "race memory" of the Furies that various species possess. In the first two volumes, it was more a matter of cultural ingraining, a result of growing up with horror stories inspired by the Furies, and could be overcome with a modicum of concentration. In TFF, though, it's treated more like a genetic memory, an instinctive response written into our very DNA, and is shown to be completely debilitating and almost impossible to overcome. There's also a timing problem relative to The Soldiers of Fear. It's supposed to be right after that novel, with a character falling through a wormhole from one book to the other; but that book is set aboard the E-D before Generations, whereas this book is set after "Learning Curve," whose stardate is significantly after GEN. However, a later reference in TFF puts it several weeks after TSoF -- perhaps there was an attempt to correct the timing discrepancy but they missed the initial reference. (Internal inconsistencies aside, this could be easily enough rationalized by assuming the wormhole had a forward time displacement of a few months.) Also, the book refers to the events of First Strike as though they took place during Tuvok's tenure under Captain Sulu on Excelsior (an interesting touch, since that was from an episode that hadn't even aired yet), when in fact they took place 26 years earlier, just after "Friday's Child," while Sulu was still a lieutenant on the Enterprise and Tuvok was three years old. As far as overall VGR/Trek continuity: The book portrays B'Elanna as overly Klingon, spouting oaths like "Kahless's beard!" and "Blood of my enemies!" which are completely out of character for her, especially for first-season B'Elanna. It describes Janeway as a former engineer rather than a former science officer. And it misinterprets the metaphasic shield from TNG's "Suspicions" and "Descent" as allowing a ship to survive within a star, rather than simply within its corona. I actually think it's a good book overall. In particular, it does a great job with the "facing Janeway with an impossible moral dilemma" kind of story that was a hallmark of VGR's first two seasons. But it needed another editing pass to reconcile it with the other books. As it stands, it's an entertaining and thought-provoking story but not one I can really "count" as part of the continuity.
Absolutely nothing. I'm just playing devil's advocate, maybe badly. Easily one of my favorite TrekLit books overall.