To determine which managed layers have records but no corresponding spatial feature (a.k.a mapped shape), run the following queries. Use the Link Shapes to Data Records tool to rectify this.

Conservation Sites:

select Conservation_Site.Conservation_Site_ID,
  Conservation_Site.Site_Name
from Shape,
  Conservation_Site
where Shape.Has_Shape_Ind = 'N'
  and Shape.Deleted_Ind = 'N'
  and Conservation_Site.Shape_ID = Shape.Shape_ID
order by Conservation_Site.Conservation_Site_ID

Element Occurrence:

select EO.EO_ID
from Shape, EO
where Shape.Has_Shape_Ind = 'N'
  and Shape.Deleted_Ind = 'N'
  and EO.Shape_ID = Shape.Shape_ID
order by EO.EO_ID ASC

Managed Areas:

select MA.Managed_Area_ID,
  MA.Managed_Area_Name
from Shape,
  MA
where Shape.Has_Shape_Ind = 'N'
  and Shape.Deleted_Ind = 'N'
  and MA.Shape_ID = Shape.Shape_ID
order by MA.Managed_Area_ID

Source Features:

select Source_Feature.Source_Feature_ID
from Shape,
  Source_Feature
where Shape.Has_Shape_Ind = 'N'
  and Shape.Deleted_Ind = 'N'
  and Source_Feature.Shape_ID = Shape.Shape_ID
order by Source_Feature.Source_Feature_ID