Invasion! is compatible. (There's a reference to the Furies in SCE: "Ring Around the Sky", and one of the characters from Time's Enemy appeared recently... I believe in the first DTI book.)
Millennium is mostly compatible - I'm not sure the epilogue is anymore.
On the other hand, since said epilogue concerns (at least implicitly) the possibilities of travel and interaction between multiple timelines and realities, all interconnected through the Celestial Temple, it pretty much fits regardless.
I relate to the epilogue the way I relate to the Garak story in Prophecy and Change -
as something that doesn't take place in the same "reality" as the mainstream novel 'verse, but is relevant to that continuity regardless, because of its context and how the setting describes realities of the Trek multiverse that transcend simple notions of space and time. (I hope that makes sense to everyone). I suppose it's not too far removed from how the Myriad Universes
story Places of Exile
is directly relevant to the prime continuity even though its events "never happened". Or, for the continuity-obsessed reader (like myself) how all the MyU
and Mirror Universe
novels are relevant to the Novel 'Verse even as they stand outside its primary continuity.
As for Invasion
, I think it's a "Broad Strokes" thing, like with Stargazer
or New Frontier
- references (like those in SCE) demonstrate that those events happened, that those stories took place in the "mainstream" continuity (and that Furies and Unclean are considered, at least, to have existed in the mainstream novel 'verse) but not all the details add up exactly.
For my part, I like to keep Time's Enemy
as part of my "personal reread continuity" and ignore the rest of the series, while assuming something vaguely like them happened. But that's me being picky, because Time's Enemy
is the only one I really like.