Can a commish delete picks that represent certain keepers?

Yes! Commissioners should first make sure that all teams have their keepers set. This will prevent those players from being available in the player pool during the draft.

To remove a pick that represents a keeper in the draft, commissioners should go to League » Settings » Edit Draft Order and choose the "Edit Rounds" button at the bottom. Select a round to edit, and then use the drop-down in the Owner column to select the [Delete Pick] option from the list and then Save. The owner will lose their pick in that round, and one will get added to the end of the draft so that they still get all of the picks they need to fill their roster.