The pencil with a line through indicates, that these swatches are not editable.
However, they should be selectable and you can apply the swatches to objects.
You should also be able to change their order by moving them in the Swatches Panel.
A pencil with a line through it represents that these swatches cannot be edited. But you can select these swatches and apply it to any page item.
Can you, please, elaborate your scenario? Are you not able to apply these swatches to objects?
Thank you, I shut down last night, the issue seems to have corrected itself. I could not apply the swatches either, just those without the pencil/line, so I thought there was a connection.