Jose wrote

Under what circumstances are pilots required to calculate an
accelerate-stop distance, and take off only on a runway that is longer
than that distance?

This runway was longer than the required accelerate/stop distance.
Vr is normally higher than V1 (but not always), it cannot be less
than V1. Once past V1, there is no guarantee that the airplane will
stop on the runway, in fact, if it is exactly a balanced field, it
will not stop on the runway.

He was simply past V1 and probably past Vr when the problem was
recognized.

Bob Moore