If planet B approached your Earth like planet A to the point that B's apparent diameter was the same as, or larger than the apparent diameter of the primary star, it would be close enough to cause gravitational interaction with A.
Occluding the star for three days would cause sharp global temperature drops, which would in turn cause global weather, like storms and hurricanes. Lots of snow would fall, changing the albedo of some areas and possibly causing temperature effects that would last for years. It might even trigger a mini ice age each time.
Large bodies of water won't change temperature much. They hold an amazing amount of heat. But surface waters will freeze. This means that ponds and small lakes will freeze over, large lakes and even sea shores will freeze to some extent.
All in all, I don't think it would destroy life on A. Earth has certainly endured worse. If there's a technological civilization, they're likely to be prepared for it.
If B is fairly small, the gravity effect would probably be that B would either become a moon of A or just smack into it. If it was moving fast enough, the net result might be that both A and B's orbit would change. But if it's moving that fast, it's not likely to hang around for days or even hours.If B is fairly large then either it will suck up A or A will become a moon of B. Another possibility would be that A's orbit will change, making life there either more difficult or impossible. I suppose it's possible that it might shift A to an even more temperate orbit.
Another possibility could be that A is already a moon of B with an orbit so highly inclined that it rarely passes through B's shadow. Depending on its orbit, it might dip into the penumbra occasionally, and once in a millennium or so, pass directly behind B. Having this period last hours or days sounds pretty reasonable. It would mean that A's orbit was wide enough to keep it from being heavily affected by B's tidal forces and magnetosphere.
Have you ever seen the movie "Pitch Black"? The story takes place on a moon of a gas giant. It has constant daylight moon wide for 22 years then an extended period of darkness. This scenario required more than one local star, though.