This question hinges on the trick: VERB tense isn't an ISSUE.
The real hidden issues are:
*
(1) essential vs non-essential modifier. (If you don't know these, Google is your friend)
* (2) parallelism within (1), preferrably showing contrast
Here it is obvious that the modifier "considered extinct for over fifty years and actually thriving in a remote part of the Andes" is ESSENTIAL as to explain the "remarkable comeback". "Extinct for over fifty years" and "actually thriving in a remote part of Andes" are contrasting points. It's preferred here to use a contrasting conjunction such as "yet", but", "however", "despite x, y" and etc..
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.
1 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.
=> Essential ModifierNo preferred contrast => Eliminate2 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.
=> ", which" is an Non-Essential modifier => EliminateShows contrast3 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
=> ", which" is an Non-Essential modifier => EliminateNo preferred contrast => Eliminate4 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.
Modifier went into the actual sentence, by definition ESSENTIALShows contrast5 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.
Modifier went into the actual sentence, by definition ESSENTIALNo preferred contrast => EliminateBonus Mistake: "remarkable comback" is a consequence of "actually thriving" thus those cannot be stated in equal priority - parallel.
Answer: