When a linked instance is used in a consuming document, you can use overrides (style and appearance, resize and layout, and structure) to customize the local instances in the consuming document.
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I've got library (file A) components linked in another document (file B).
If I apply overrides (eg: size) in file B, then paste these layers into file A, these overrides are stripped out, and the components appear in their original master state.
Desired behaviour:
If I've made changes to a component I want them to be reflected if I copy and paste layers.
If I copy and paste within file B, the overrides ARE retained.
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When a linked instance is used in a consuming document, you can use overrides (style and appearance, resize and layout, and structure) to customize the local instances in the consuming document.
If you modify and save the master component in the source document, a blue badge
next to each linked component instance in the consuming document indicates that an update is available. You can hover over the blue badge to preview the updates within the Assets panel, and if visible, on the design canvas.
Click the blue badge to accept the updates to an individual component and click Update All at the bottom of the Assets panel to update all instances within the document. For more information on linked assets, see Work with linked assets.
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I have the same problem as the OP.
I've tested this on 2 new documents.
To me I suspect this is either a bug or a weird feature.