Hi Neergaard,
Yes, you are correct. My original suggestion was wrong. You will have to delete the the original sections in the custom script.
If you assume that 1) element-section assignments have not changed and 2) all shell sections are being updated, this should be feasible.
Some background on why we append instead of overwrite:
Overwriting sections in Abaqus is difficult when elements are assigned to new sections (indirectly via elsets). For example if you create or modify a component in HyperSizer, this leads to a new elset in Abaqus. Things get complicated when the modified elset is referenced elsewhere in the model. For example, perhaps the original elset was used to apply loads or boundary conditions. Things also get complicated when only a subset of the elements in an elset are being updated. For example: only half the elements in an element set may have updated properties from HyperSizer, the other half need to preserve the original properties. For Nastran we don't have this complication because each Nastran element is assigned a property ID. There is no layer of indirection.
For now we error on the side of caution and only support SGS. Eventually we would like to support SS because we know that it is more general and more popular.
-Ryan