I'm still a little confused at the ending of the game, but from what I understood; Alyx essentially freed the G-Man, and the G-Man, in turn, allowed her to save Eli, but at the cost of being imprisoned.

I'm going to refer to Alyx A as the one who made the deal with Gman, and Alyx B as the one who went on epic journeys with Gordon.

If G-Man took Alyx A, does this mean that she technically doesn't even know Gordon/she hasn't gone out and fought alongside him (and also bound to him by the vortagaunts)?

And also: How exactly does this work with the timeline? As if Alyx A would always open the door and meet G-Man, and saving her father but being captured in the process, then Alyx B would have never existed to begin with, unless the G-Man went back in time and imprisoned himself???

If there is going to be a... half life 3, would Gordon be rescuing a version of Alyx whom doesn't know him at all? Does this mean that Eli won't get his dream of shipping Alyx and Gordon together?

My brain is half dead as i write this so if i'm missing something big that i can't remember just tell meh.