Question: In the year 2500, the main planets are all colonised for various reasons (Mars as another place to put the population, Mercury for minerals, etc.). The planet Mercury then becomes more and more rich, until its ruler declares himself emperor. 

In the year 2900, a war starts, lasting until 3000. At the end, people have been reduced to almost stone-age technology. My question is this: how would someone attack in a way that the people survive, while knowledge disappears.

Answer: 
Depends on the level of technology. For simpler technologies you cannot get rid of them without killing people. People will remember and pass on. For high tech, destroy the infrastructure and do not allow them to rebuild it for a while. Additionally, destroy libraries and wipe out digital devices using EMP. This will send them back to late 1800s. Without advanced machinery, knowing how to make 22nm transistor will not help anyone. Over time, people will switch to a more primitive technological level and will start building slowly. Not having books means not having head start as most primitive technology will not be known to the people. With war running 100 years, most people with the knowledge of the advanced machinery will die of old age. Even if they manage to get back into advanced age, they again will not have any head start to rebuild. Then these people will slowly advance like we did in the past.
Other Galaxies
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Probably not because unless there was a crazy breakthrough in technology that would allow us to explore all of the other galaxies in this universe. And plus we don't know if there are or aren't any other planets in our universe that are as technologically advanced like us. And the only way to remove all technology in the universe would be by somehow exploring every part of every galaxy in the universe, and removing all living species and removing all the technology that they have.

Constants
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Even if this were to happen we would be operating technology at the moment of trying to remove all technology, making it almost impossible to ever complete such a feat, and an exponentially less chance in 100 years.