I rewatched Endgame for the 2nd times with some friends and do you know what really bothered us (one shipped J/C, the other J/7 & me who shipped neither of them counted points while noting that something was wrong) in the 2 parts episode? It's the fact that Janeway seemed not to know what was going on behind her back, with reference to C/7, whereas Chakotay was her close friend/confidant (and we can suppose that Janeway is the same for him) and Seven, her “surrogate" daughter... I mean, look at how Janeway seemed to be flabbergasted when her older doppelhänger told her about them -> she was as much shocked by the news of them as a couple as the death of Seven!
)
Seriously, couldn’t the writers of Endgame have foreseen a short sequence in the 2 parts episode to show us C or 7 informing Janeway of the romance (1), instead of all scenes where C/7 going sweet (2) or even 7/Neelix (don’t get me wrong, I was happy to see our Talaxian hybrid again but I thought that wasn't he closer to Janeway than Seven!)?! Unless the scene existed and the producers/director decided to delete it for saving time or because they judged it superfluous... . BUT meanwhile, this "missing scene" let us believe that our Romeo Juliet hid from Janeway. It wasn't accurate to what we know of Janeway and her relationships with Chakotay and Seven, if you want my opinion!
About Chakotay :
Let me be clear here. I don’t say that he was accountable to Janeway when it concerned his sentimental life - though I note that he has never been shy to ask questions about hers! – but well informed about the almost filial relation between J & 7 (I don’t doubt that the ex-Borg’s was often at the heart of conversations between the both leader officers as well in formal settings as in private, right?!), he would have informed his friend of the situation and asked her if she was OK with it, especially after to have declined her invitation to luncheon to join his date, while it was clear that Janeway had need for companionship! 2 possible result: At best, Janeway indicated to him that she already heard about him and 7 - and encouraged him (the fact that J has the most “knowledgeable” about Seven could even help him!). At worst, Janeway expressed her reserves, particularly with regard to Seven’s emotions and she adviced to wait.
About Seven:
Did Seven be afraid to hurt or betray Janeway (and we know how badly she react to betrayal, in particular when it comes from someone close to her -> cf to her speech to Tuvok in Prime Factors), she kept silent? I mean, Janeway is the one - with the Doctor -, who worked very hard to ensure that the ex-Borg reclaims her individuality and humanity, when Chakotay distrusted her most of the time, calling her Janeway's "personal project" or something like that (same for Tom Paris, besides). Even if Seven has gone visiting her mentor to say: "thank you for everything, Capitain, but from now, I shall need you no more. It's Chakotay, my newly boyfriend who will takes over you now", it would have been better than to let Janeway hear it by Tuvok (even Neelix knew & advised her or the Doctor had to guess who was her love interest) or worst, by others crew officers, right?!
We can think what we want of Janeway but the character deserved better, as someone whose loyalty to her friends and her crew was never lacking AND as Captain, who always guarded that order & discipline are present aboard but in the respect for each.
-> We learnt from Adm. Janeway that her younger self has accepted the relationship between Chakotay and Seven, going as far as marrying them and supporting Chakotay after the premature death of Seven, so ...
On the other hand, I adored the episodic confrontation between Admiral Janeway and Capitain Janeway... Even if at the end, they are only one Janeway, not leaving !
.
Mulgrew really made a great job there!
I guess that the duel Janeway vs Janeway didn't leave place in the romance for heranymore, that she is young or hurdy-gurdy! 
(1) By contrast, the authors of fan fictions, whatever is the shipping (J/C, J/7, C/7) weren't lacking this "missing scene". It wasn't a big deal but it was important and well, I'd have liked watching it.
(2) At the end, in spite of the insistence of writers to convince us that their romance was a serious affair, we (a great majority of fans/actors themselves, which is worst!) don’t believe in it more now than 15 years ago.

Seriously, couldn’t the writers of Endgame have foreseen a short sequence in the 2 parts episode to show us C or 7 informing Janeway of the romance (1), instead of all scenes where C/7 going sweet (2) or even 7/Neelix (don’t get me wrong, I was happy to see our Talaxian hybrid again but I thought that wasn't he closer to Janeway than Seven!)?! Unless the scene existed and the producers/director decided to delete it for saving time or because they judged it superfluous... . BUT meanwhile, this "missing scene" let us believe that our Romeo Juliet hid from Janeway. It wasn't accurate to what we know of Janeway and her relationships with Chakotay and Seven, if you want my opinion!

About Chakotay :
Let me be clear here. I don’t say that he was accountable to Janeway when it concerned his sentimental life - though I note that he has never been shy to ask questions about hers! – but well informed about the almost filial relation between J & 7 (I don’t doubt that the ex-Borg’s was often at the heart of conversations between the both leader officers as well in formal settings as in private, right?!), he would have informed his friend of the situation and asked her if she was OK with it, especially after to have declined her invitation to luncheon to join his date, while it was clear that Janeway had need for companionship! 2 possible result: At best, Janeway indicated to him that she already heard about him and 7 - and encouraged him (the fact that J has the most “knowledgeable” about Seven could even help him!). At worst, Janeway expressed her reserves, particularly with regard to Seven’s emotions and she adviced to wait.
About Seven:
Did Seven be afraid to hurt or betray Janeway (and we know how badly she react to betrayal, in particular when it comes from someone close to her -> cf to her speech to Tuvok in Prime Factors), she kept silent? I mean, Janeway is the one - with the Doctor -, who worked very hard to ensure that the ex-Borg reclaims her individuality and humanity, when Chakotay distrusted her most of the time, calling her Janeway's "personal project" or something like that (same for Tom Paris, besides). Even if Seven has gone visiting her mentor to say: "thank you for everything, Capitain, but from now, I shall need you no more. It's Chakotay, my newly boyfriend who will takes over you now", it would have been better than to let Janeway hear it by Tuvok (even Neelix knew & advised her or the Doctor had to guess who was her love interest) or worst, by others crew officers, right?!
We can think what we want of Janeway but the character deserved better, as someone whose loyalty to her friends and her crew was never lacking AND as Captain, who always guarded that order & discipline are present aboard but in the respect for each.
-> We learnt from Adm. Janeway that her younger self has accepted the relationship between Chakotay and Seven, going as far as marrying them and supporting Chakotay after the premature death of Seven, so ...

On the other hand, I adored the episodic confrontation between Admiral Janeway and Capitain Janeway... Even if at the end, they are only one Janeway, not leaving !

Mulgrew really made a great job there!


(1) By contrast, the authors of fan fictions, whatever is the shipping (J/C, J/7, C/7) weren't lacking this "missing scene". It wasn't a big deal but it was important and well, I'd have liked watching it.
(2) At the end, in spite of the insistence of writers to convince us that their romance was a serious affair, we (a great majority of fans/actors themselves, which is worst!) don’t believe in it more now than 15 years ago.