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I applied gaussian blur on several layers and after pre-composing effects disappears. what can be done about it?
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This is to be expected. that's simply not how it works. If you want to pre-compose something, you have to include the actual layers underneath so there is something to process. Some effects work with the continuous rasterize/ collapse transformations switch and pass through their operations, but not all of them and that's the crux of it. You need to adapt your workflow.
Mylenium