I'll start with Earth
Earth is hurling through space at a speed of approximately $29.78 km/s$ If the sun were to disappear, the Earth would move in a straight line until the sun reappears. Since there are $259,200 seconds$ in three days that gives Earth the time to travel $29.78 km/s \times 259,200 s = 7,718,976 km$ That's quite a distance.
Since the distance between the Earth and the sun varies between $147,098,290 km$ and $152,098,232 km$, I'll average that down to about 150 million kilometers for calculations.
Using Pythagoras, we can get the distance form the sun when it comes back after 3 days: $\sqrt{150,000,000^{2} + 7,700,000^{2}} = 150,1632,44.504$. This puts us about $160,000 km$ out of orbit, peanuts compared to the difference between the Earths aphelion and its perhelion which is about 5 million kilometer.
What about the influence of other planets?
Good point, Jupiter is huge and can get reasonably close to Earth [citation needed]. We'll assume a worst case scenario and place Jupiter at a distance of 600,000,000 km from earth. Jupiter is significantly slower than earth, but in the span of three days, this is not going to make a huge difference considering the distance between them.
You can calculate the acceleration of a body under gravitaional influence by another body as: $G\frac{m}{r^{2}}$ Where G is the gravitational constant, m is the mass of the body attracting (Jupiter in our case) and r is the distance between the two bodies. Filling this in gives us: $6.673\times10^{−11}\frac{1.8986\times10^{27}}{600,000,000,000^{2}} = 3.51926606\times10^{-7} m/s^{2}$ Which means that the earth will accelerate towards Jupiter at a rate of 3.51926606*10^-7 m/s every second. After 3 days we will have traveled $\frac{3.51926606\times10^{-7}\times259200^{2}}{2} = 11822.0311653 m$ towards Jupiter, not even $12 km$!
Mars is closer though.
I see your point, but assuming Mars is as close as 50 million km, we get an shift towards Mars of about $56 km$. Not really significant.
How will other planets fare?
Well, Mercury will be off the worst. If there's no significant change there, there won't be a significant change anywhere. As it is traveling at about $47.362 km/s$ It could travel a distance of more than 12 million km in 3 days. Taking into account its smaller orbit, this would take it about 1.2 million km out of orbit, not bad. But still not much compared to the variance in its orbit which is almost 14 million km.
Conclusion:
If Fernir eats the sun, there are more important things to worry about than where the planets will be in 3 days, when Fernir needs to go to the bathroom.
Edit:
But wait, the Earth is now going too fast for its distance from the sun
You're right. And it's slightly turned away from the sun too. And I must admit, I underestimated the effect of this. As some intelligent people in the comments pointed out, this would change the eccentricity of the earths orbit from 0.016 to 0.06. Using this calculator we can then figure out that Earths orbit will now vary between 141 million km and 159 million km. The difference has nearly quadrupled! In the grand scheme of things, our orbit will still be relatively similar, this might be enough to seriously influence weather pattern though.
Another possible effect.
Since gravity can not travel faster than the speed of light, the effect of the sun disappearing can only propagate with the speed of light. Gravity needs about 4 seconds to traverse the diameter of the sun, so gravity will drop from 100% to 0 over the course of 4 seconds. Additionally, there will be about a 0.04 second lag between the part of the Earth facing the sun and the most distance part. The acceleration due to the suns gravity is $\frac{6.67\times10^{-11}\times1.9891\times10^{30}}{(1.496\times10^{11})^{2}} = 5.928151\times10^{-3}m/s^{2}$. Dropping from this value down to 0 over the course of 4 seconds with a maximum lag of 0.04 seconds doesn't seems bad enough to cause anything major, but maybe it is enough to cause some earthquakes? I'll leave that to geologists to decide.