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My brother just received a letter from the pension plan stating that "the retirement request cannot be processed because the returned paper work was incomplete."
The Benefits Administrator included a payment election form, a rollover form, and a proof of estate form, specifying in each case that he use a Estate's EIN in place of her social security number.
My questions:does an estate automatically exist, or will he have to establish one? Is this necessary?
Yes, an estate "automatically exists," but the fact that the benefits administrator is concerned about the estate having an EIN (actually a TIN) suggests that there's more going on here than you have explained. Since we obviously know nothing at all about your sister's pension plan, there's no way we can provide any intelligent opinions about it.

If your brother can't figure this out, then he should consult with a local probate attorney.