After playing catch-up, and reading everyone’s posts since I’ve been here last, I guess my opinion is this:
Since the avatar, no matter which Vik is replaced, can make a healing flip, it means that when it is manifested the avatar is activated (since it is the one making the flip), thus if it replaces the Vik that made the (all) action it is done after the flip (which I think we all agree on). If it replaces the unactivated Vik, then it doesn’t get any general AP (as the unactiveted Vik never generated any, and the Avatar is already activated), but I think that it would get the 0 and the +2 Melee Master AP. This was suggested by someone above, don’t remember who (and don’t feel like looking it up), but I think that this is the best compromise between RAI and RAW.
As far as the “wording on card is that 1 is replaced and 1 is removed” vs “both are replaced and thus both subject to replace rule”, the only thing that gives me pause as to Omen’s argument is that the wording on the card is different than the wording in the rule such that you can replace the unactivated model, where as I think with the replace rule it is working on the assumption that an activated model is being replaced (the activated model is replacing itself with something, which is possibly not happening in this case). Coming from Warmahordes, and the rules system that is used, if one effect is supposed to have the same effect as another, then the same name is used; for instance the spells Chain Lightning and Ashes to Ashes – these two spells are very similar in nature (both generate d6 attacks, both require attach role for the initial hit) but the way they work is subtly different; if it was intended that they work the same they both would have been called Chain Lightning (or ashes to ashes). In this case, I think that if “replace both Viks and subject them to the replace rule” was meant, then that’s what the card would say (replace both Viks). But since the card says “replace 1 vik and remove the other”, it’s rather muddy. I guess my point is that if the card was supposed to mean “replace both” then that’s what it should say, given other cards out there state that when that is what the card means. Or, on the manifest steps, it should say something like “this model may immediately make a healing flip, then its activation ends.”.
But I could be completely wrong. as such, i think i'll take omen's example, and play how i stated above until either a) my opponent strenuously disagrees or there is a ruling (finally) on it. you'd think that after almost a year of debate that this issue could be resolved; there aren't any new points being brought up and all that has to happen is a decision that "this is how it is going to be played: blah". i'd settle for a coin flip at this point.