Are you saying that when you toggle the overlays, your mesh disappears in the areas that it has face sets or masks? If so yeah that shouldn’t happen I think. You can clear masks with ALT + M and face sets like Dwayne said. Just in case, overlays shows or doesn’t show all the overlays of the 3D view, so in part that it what it does, but it doesn’t hide the masks along with it.
Just in case you have a bug, try copy pasting your mesh into a totally new scene and see if the hiding problem persists in the new file.
