Unless you go to the ridiculous levels of Mirror Universe type coincidence (somehow all of the same characters are together and interacting even though their history is so insanely different), I don't see any way Voyager would be recognizable in the new timeline.
I don't even think it is likely Voyager would exist at all.
It's just as unbelievable that the same crew would all be on the Enterprise with the same ranks and positions. Yet it happened.
Apparently Trek follows Farscape's time theory: If you get things as close as you can to how they were time will re-align itself to be as close to the prime timeline as it can.
I realize that. The precedent is obviously there. It's just an idea I personally don't really like. For me, despite all of the unbelievable stuff that happens in Trek, there are certain things that stretch things a bit far for my taste. This is just one of them. I realize everybody doesn't feel like that.
I don't agree that the timeline does or even should be working towards realigning itself with the "prime" universe though. Of course what I want and what the Trek stories and universe actually do are two very different things!