Thanks! There's an undocumented feature released a few days ago that is supposed to reconcile with the source mesh, more info here: https://splitpainter.itch.io/vertex-studio/devlog/1590929/new-version-10-beta3-b...
I haven't tested with changing the mesh vertices themselves though, only the UV, so please backup your scene first before trying. I'll also give it a try and report here next.