I tend to avoid theorising about Skuld. Ever since Nomura nixed her from Back Cover (including the one scene she absolutely should have been in) I have no idea what the end game is for her and thus disregard her from the equation.Ava being Subject X is pretty much contrary to all the hints we've received actually, along with that Dandelion Meeting Q&A with Nomura last year April 2018.
Tbh, disregarding Skuld in the equation as to who jumped worldlines, and who's who pretty much makes this interview, the KH3 Secret Reports, as well as the motif parallels with Lea and Isa, contradictory. If she isn't Subject X, then what happened to her?
But that doesn't mean we don't have hints on what happened to Ava. Luxu hinted it by saying that she carried out her mission, and in the Japanese version, he said she totally completed her role. So that could either mean she is working in the background doing her own thing now that's she's free from her role, or she might've vanished just like Sora due to her role.