So the on-again, off-again status of Iran cooperating with international investigation specifically with respect to proper handling of the CVR and FDR is affected in what way by the in-fighting (per NYT's reporting) between power centers or factions within their government and military hierarchies? The multi-national group convened by Canada seems conspicuous by omission in the Times article.
The possibility of a more deliberately overt, and obviously far more malevolent, act wasn't ruled out before the NYT reporting. And its reporting still does not warrant ruling out such a more sinister truth. Not conspiracy theorizing, rather just bitterly skeptical when a story is recited but appears not to add up in one or more ways, and could plausibly (or more than only plausibly) turn out to be a cover story.
A few years ago, at an official conference of a major organization in international civil aviation I had the chance to meet two staff members from Iran's Civil Aviation Organization, a Director in Air Navigation Services and Aerodromes; an Assistant Director also. The mostly small-talk conversation was cordial enough. I wondered how significantly their career paths and actual roles and responsibilities were as professionally appropriate as they were in conversation, rather than having been dictated by what is usually called a theocracy. As to what these young men - both appeared pretty early in career years - would say about the black boxes, in their professional capacities, we only can wonder, guess, and hope.