I would argue that Season 6 would have looked quite different with both VOY and Equinox in the picture.
The writers would have to come up with events that involve both ships on joint or separate missions, different events on what happened - exploration of Equinox survivors and how they are adjusting to the 'new' Equinox (and its new crew). etc.
Even if they had Season 6 fleshed out more or less and changed their minds about keeping Equinox around at the last minute, they could keep a few episodes as they were, but ultimately, both S6 and 7 would have to take a different route.
Also, (for example), in my story, I have 0 intention of destroying Equinox mid S6... its gonna stick around.
Perhaps. But with the Equinox surviving, there's just a domino effect that would likely start rolling.
Depending on how the writers approached character and events development - if the audiences received the Equinox and its new crew 'well enough' and the altered dynamic between the two ships (and stories that follow) its possible it would have resulted in a lasting change.
Its not impossible to tell stories between 2 ships/settings effectively and make it last. Ds9 did it, and other shows did too.