Its hard to say....
So many ways that SO 937 could come around... Prior to Prometheus the company knew something but we could not be sure to what level they knew.
Prometheus Viral Campaign gave us information that prior to Prometheus they was aware of a signal and David was to monitor this and only he would be in the know... we have to assume Weyland would too.
LV-223 aftermath such as the likely hood of a investigation is also now a plausible way the company could get some knowledge but it would appear to match Alien they would not be 100% in the know as much as David is in AC.
And so also Alien Covenant aftermath also gives another option for how Special Order 937 could come about...
But i dont think anything is known to the Covenant Mission at the time they set off.. I dont think the company would be aware of Davids Location.
But who knows.
