"account for" means knowing, or having a record or an explanation for, the fate and whereabouts of something or someone.

Regarding the files, "accounted for" means you have a credible record or explanation as to their fate or whereabouts. Files destroyed, if you have a credible record of their destruction, are also files "accounted for".

No, it does not mean that they have been found. They could all have died in an explosion in outer space and it could be that you just had incontrovertible evidence that this was so and you had not been able to retrieve bodies nor any debris.

Basically, yes. "Accounted for" means that authorities now what happened to all passengers. They have been identified etc.