No doubt! Poor BXVI - one insult following another.
Francis essentially said, in his letter, that he regretted having to accept the resignation because Vigano had been doing such a wonderful job and therefore, in order not to lose such an excellent and knowledgeable person, he was creating a special new position for him (second in command to the very same office that he messed up) so that he could continue to assist the department. Hardly a resignation or even really a demotion.
So in other words, Francis is signaling that hes on board with the whole thing and it was all cool.