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.