I had this very same issue last week. It just randomly happened. I'm almost 100% certain that I did no tinkering for the problem to occur.
I had to completely reinstall Aerofly for everything to comeback. At first I performed an Integrity Check but that did not fix anything. However, I believe you might be right about it being an xref issue? I can't fully confirm because I went straight for the reinstall fix. But it might just be that you need to reinstall those xref folders?