(A) The rare bird, considered extinct for over fifty years and actually thriving in a remote part of the Andes, has made a remarkable comeback over the past decade.
but is required in the sentence and the different usage in tense of considered and thriving adds on to the sentence expulsion
(B) The rare bird, which had been considered extinct for over fifty years but it was actually thriving in a remote part of the Andes, has made a remarkable comeback over the past decade.
it appeareance isn't correct and also the usage of which
(C) The rare bird, which was considered extinct for over fifty years and had actually been thriving in a remote part of the Andes, made a remarkable comeback over the past decade
The usage of which isn't correct and the absence of but before had also adds on to the meaning of the sentence
(D) The rare bird was considered extinct for over fifty years, but it was actually thriving in a remote part of the Andes, and, over the past decade, has made a remarkable comeback.
This is exactly the intended meaning therefore let usa hang on to it
(E) The rare bird was considered extinct for over fifty years, was actually thriving in a remote part of the Andes, and, over the past decade, has made an remarkable comeback.
an usage beside remarkable isn't right and distorts the meaning
Therefore IMO D