After errata and rules update, ECM text says:
Once per turn, after an enemy group has allocated Attack Dice, you may pick a friendly ship within 4” of the
Calypso. Add 1 to the lock value of the groups Attack Dice allocated to this ship. Subsequent
attacks by other groups are not affected. In order to be affected, ships must be on the same layer as Calypso.
I would argue that because you pick friendly ship in 4", that ship is the affected ship and therefore only that ship is required to be on the same layer.