Shell features need to be planned very early in the design process as they effect the entire part.
Is this part from a casting?
If so, perhaps you can design it like a casting, that is, do not add any machining features until after the casting is modeled.
or
make the features to be shelled early in the feature tree
or
make the features to be shelled as New Bodies with multi-body solids techniques and then Combine later in the feature tree.
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