Unreconciled layers are layers that have been added to the drawing or to attached xrefs since the layer list was last evaluated.
To reconcile a layer in the drawing you have to manually select it and mark it as reconciled.
All layers that have been added to the drawing or its xrefs since the last user-specified action (for example, reloading an xref), are listed.
This will add the layer to the layer baseline and not display it as new anymore in the drawing.