I don't remember where I saw it (probably in the pre-release videos), but it was stated that the stacking faction bonus for Bounty Hunters stayed active from one phase to another. But the in-game description states that it's until the end of the encounter... so, only during a single phase.
Did it change from the beta/dev-build info, or is it a typo in the raid description?
Also, if a BH dies and is revived, does the stacked bonus remain? Or is it reset?