I think the plan was to make TWO more Sequels and they had a certain direction and broad Plot idea for how these movies would directly carry on from Alien Covenant and lead to Alien.
But the performance of Alien Covenant could indeed make FOX have to Re-assess the situation, i would assume they wanted to get the next TWO movies done rather quickly and would assume had all gone to plan, Production for the next one would have been under way this year, shooting next year sometime with a sequel Lined up after that. And so i would assume we would have had a like 2-2.5 year gap between Alien Covenant and the Sequel and likely the next sequel 2-3 tops after that.
Now i think they are going to look at why Alien Covenant did not do well, and see what they think needs changing as far as where to take this Franchise now.. I think any Production Plans could be put on Hold while they assess how the movie does during its Home Release.
I think for sure Alien Covenant will get a sequel and i would even think we would see it within 3 years but i am not sure if we are going to get the as Planned TWO Sequels to Alien.. i think they will now either make a Covenant sequel and actually have it that it does not connect to ALIEN but will show enough and give enough clues that would provide us with Answers to what happened to lead up to Alien.
Or they will make the Next Movie connect to Alien more Directly and so Cut their TWO Movie Route to Alien into a ONE Movie Route.
so they can put this whole David angle, and Prometheus links behind them and then likely carry on with a sequel set after Alien for sure within the Franchise.
This is all just my assumption.