So much versions were given over the years (not necessarily maliciously from contemporary witnesses), but basically, no matter that Mulgrew decided to reject J/C as a potential and sustainable couple from the beginning or from s3* (preferably before Resolutions), the relationship confined itself to a deep friendship and as I oftenly repeated, this was fine with me (I know, a few of us share this opinion but well...

).
*even if Mulgrew has agreed to let her character of Janeway play, loving feeling with Chakotay, this has never been beyond of mutual flirtation, particularly in the beginning (but "Resolutions", in s3, nipped the potential love story in the bud), the actress thought that thereafter, it was too late (and in any case, if something must have happened between them, it would have happened for a while, dixit Mulgrew herself) . And let's be honest, it would have been very strange to see, in Endgame, no matter the part 1 or 2, Janeway rushing into Chakotay's arms, finally confessing her regrets to have waited so long then her everlasting love, after she has politely rejected his disguised advances so many times before and moreover in last seasons, where she has indicated a total indifference to him.
-> well, I know that this is what was done with Chakotay/Seven's romance but please, note that neither producers or scriptwriters wanted to insist on or push too much on this turn of events (maybe because a part of them knew that this part would shock a lot of people...), and besides, in the 2nd part, there will be a very few intimate scenes between these both characters (that is they hardly looked lovingly at each other and that, until very the final scene). In fact, I'd say that the viewer came almost to wonder if they were still together at the end. Was it wanted or accidental?
As for the question of Janeway and Chakotay kissing, well, I don't know (plus, where are the said deleted scenes?). Have you ever noticed that these juicy details were often given to people and some medias particularly drawn to these kind of stories, no matter where they come from : stars, co-stars, insiders or invented by reporters themselves, for the only goal to excite, here the J/C fandom, keep the flame alive or make people purchase/read their papers?! You know, it's like the rumors about the supposed short romance between Mulgrew and Beltran in first seasons. There was no proof in those days and still now, both actors are silent about this story and people like Wang, who seems to adore to exude details on behind the scenes, never said anything about Mulgrew/Beltran.