Family Table assembly part structure mismatch

I have a family table of parts with 33 variants. I have a second family table of 33 assemblies that uses those 33 parts and adds a few extra standard components. 

Depending on the assembly variant, certain sub components are turned on and off - hence the QTY changes.

I've used the "compare to part" utility to update my WT parts with the structure from the CAD. This seems to have set the QTY of sub parts from the generic as the quantity for every variant, even when there are less.

I'll put some numbers and names to it:

Parts

Family Table:

   (

   Plate Generic

   Plate 1

   Plate 2

   ....

   Plate 33

   )

Cover

Rivet

Assemblies:

Family Table

   (

   Plate Assembly Generic

        - Plate Generic x 1

        - Cover x 4

        - Rivet x 8

   Plate Assembly 1

        - Plate 1 x 1

        - Cover x 2

        - Rivet x 4

   Plate Assembly 2

        - Plate 2 x 1

        - Cover x 4

        - Rivet x 8

   .....

   Plate Assembly 33

        - Plate 33 x 1

        - Cover x 4

        - Rivet x 8

   )

The WT part for Plate Assembly 1 shows 4 x Cover and 8 x Rivet.

Any advice on how to fix this without manually tweaking each WT part structure would be greatly appreciated.

Thanks.