Recent comments from Hawley referred to the prequels as "historical documents," so I don't expect this show to be writing the prequels out of existence by any means but I also don't think the core lingering questions (like David's whereabouts) are going to factor in.
Since we're supposedly seeing a ship in this show with a Weyland-Yutani logo (rather than a Weyland Industries one) I wouldn't be shocked if there's some allusion to Peter's Prometheus mission tanking the company to some extent and leading to the necessity of a merger with Yutani.
Also, I don't expect it by any means, but I'd definitely be curious about the presence of some sort of Engineer installation on Earth, given that they had obviously been here over the years before abandoning us...