i built a raid farm but my auto sorter keeps only taking the stuff from the non filter chest and burning everything it was working before until i added a burner how can i fix?

You should be using either a hopper line or a water stream, not both. For this I would go with water stream and double speed filters. Items should only be entering the start of the hopper line at hopper speed. As you’ve got it, parts of the line can pick up item stacks from the stream which lets them miss their filter. In the first picture, it looks like you have 2 hopper lines stacked together, which seems really unlikely to work

Why is the burner at the bottom of all those chests? That’ll burn all of it rather than the overflow. I think you want to pull from the top chest, but only if it has a high comparator reading

Could you provide more details about what you’re trying to achieve and any designs or tutorials you’re using?

I don’t understand what your issue specifically is despite reading your title and looking at the images a hundred times. A filter chest is a part of the auto sorter, so I don’t understand what it means for the auto sorter to take stuff from the non filter chest.

Now I notice a few things that are likely causing issues.

The first image is of a different build with 4 layers of hoppers and one of those layers is completely useless

The main issue is likely that you currently have a row of hoppers to distribute items to the filters. (The very top row in images 2-4), however you also have water stream disruption which should normally run items directly along the filter hoppers (the ones that you read a comparator output from). These two distribution systems are not compatible and you need to choose one or the other. I recommend removing the top layer of hoppers and using the water only to distribute items.

You have it so that items will recycle through the system once reaching the end of the water stream, so they won’t actually get sent into the last slice to be burnt.