Well, maybe because in returning in the past, Admiral Janeway erased what's happened in her timeline. Besides, it was her intention to allow Voyager and the crew to come back earlier and to save a lot of lives. I think that she knew right the beginning of her mission, that she couldn't come back in her timeline for the only reason that this one would no longer exist. Remember Capitain Braxton in Future's End , Seven from the 29th century in Relativity or Harry & Chakotay from 24th century but 15 years in the future in Timeless. None of these characters managed to return in her/his timeline. Most died in mission. On the other hand, their alter ego (from the past) took over, accomplished the intended goal...and most of the time, their fate was modified ... .
. A contrario, some people think that whatever we act, one cannot change the fate. what has to happen, will happen... I dare to think that each of us is the master of her/his fate!
It seems to me that the "original" future is that Voyager would have come home sooner or later on Earth and Capitain Janeway & Enseign Harry would have been promoted for services rendered (surely more slowly for Harry -> I cannot imagine him becoming Capitain from Enseign. in a snap of a finger!
) . Tom would have left Starfleet for the civil sector and B'Elena would have followed. Through her actions, Adm Janeway just speeded up the process, prevented certain events from taking places by the same. As for Chakotay, he was supposed to have died with Seven while Voyager was still in Delta Quadrant Please, don't hesitate to correct me if I'm wrong but I have no memory that it was clearly said that members of Maquis had been pardonned by the Federation. In fact, since Hunters (4x15), where we learnt from Chakotay who has gotten a message from a friend that Maquis was gone and their companions have been or killed by Cardassians or emprisonned in Federation's prisons, this issue was not approached anymore per se. I just remember later in the series (s6 or s7?), an upset Janeway informing Chakotay that Starfleet & the Federation still considered ex-members of Maquis as outlaws (and would be made prisoners in their return on Earth), in spite of all the reports sent where she praised their commitments in the smooth running of the crew & of the vessel during all these years. And that she would keep making every effort in order to see them all rehabilitated...
=> except B' Elena who due to her situation (daughter-in-law of an imminent admiral of Starfleet) and additionally a brilliant engineer, the situation of her friends remain unknown as far as I know or almost., as seeing as these people have left Starfleet on their own initiative (by deserting or by resigning like Chakotay): there isn't much chance that they wear again the uniform, in particular if they kept the same state of mind as before the events of Caretaker!
