Well, we were making good time right before maintenance to finish our first run through on heroic, but unfortunately we discovered this little doozy when I i died from dots after getting the killing blow. And since I was the only one alive with no way to heal myself, exactly what you explained happened to us. Unfortunately we just continued on with the trash leading up to the last boss when we discovered that the door to his lab(?) wouldn't open until we activated the bridge, which was of course, impossible.
A disappointing end to and otherwise challenging and enjoyable Flashpoint.