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When a unit with halberds and shields is within six inches of skavenslaves that lash out with the cornered rat rule does the halberd and shield unit get the extra save modifier as though being shot or do they defend as though in close combat where their halberds would impair them from using the shields?

This is when the slaves freak out after losing combat yes?
Then IMO you may use your shields as they are not CC attacks.

Yes and besides doesn't the cornered rats rule say "allocated like shooting" to further make sure.