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There is a problem I keep running into when using artboards. when I use the 'copy merge all layer' shortcut (Command+Option+Shift+E) it merges all artworks from all the artboards in the document. The only solution I have for this is to manually select and mask the merged layer and applying the layer mask - that is time lost on tight deadlines. I'm really looking forward to an update where artboards work like they do in illustrastor. If anybody has a simplier fix I'll be happy to know it.
Thanks
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Have you tried to hide other artboards before merging? Quick way is Alt + click on eyeball in fornt of artboard you want to merge. Later Ctrl + Alt + A to select all layers then Ctrl + , to show them again. This is not solution but try to help you speed up things and avoid selections and masking.