This theory has been debunked on an aviation web site I visit.I'd agree, the planes have separate registrations, and both are accounted for as being retired from the American Airlines fleet.
However, in both cases the issues of ownership and registration are somewhat opaque and mysterious.
That's typical among these fly by night airlines but doesn't imply terroristic intent. It's simply the way business has been conducted in Africa since forever. It's pretty clear ( to me anyway ) that the theft of the plane in Angola was merely a "repossesion".