And this diagnostic says exactly what?  None of us volunteers have the codes memorized.

"The following diagnostic is generating:"

Well, the good news is, at least the generator is working today.

I am trying to efile a final Form 1041 with a missing beneficiary social security number.  Will the IRS reject this return?  The social security number of the beneficiary is unknown, and the beneficiary can not be located.

Yes, the e-filed return will be rejected.

The exact wording of the diagnostic warning:    e-file:  Beneficiary/Grantor #5:  The Beneficiary Identification Number is either missing or invalid.  It should be a nine digit number, "Applied For". "foreign US", or "Form 1042S" for a foreign beneficiary.  (ref#25183).

Can this rejection error be overridden in Lacerte?

Very unlikely, but you can try.