Answered
when i try and export my threshold layer changes
the first is how i want it the second is how it comes out whenever i export or megre layers.
You need to view at 100%.
Then you will see that they are absolutely identical.
The difference you're seeing is an artifact from the screen resampling when you zoom out. 100% means that one image pixel is represented by exactly one physical screen pixel. That's the only way to see the true pixel structure of the image.
To be clear - the flattened/merged version is the correct one. The preview can be misleading, unless you view at 100%.
In a "normal" photograph this doesn't matter. But it becomes a factor with noisy and binary images like this.
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