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Company B cannot buy something which is already owned by someone else. Whether they acted in good faith or not is irrelevant.
If there is evidence that your father purchased the freehold the estate of your father owns the freehold the executor/administrator of the estate of your father should get the property transferred to them on behalf of the estate as a first registration of the land at the land registry.
A local conveyancing solicitor could do this for you at a modest cost.