In the Illustrator layer pallete, somtimes the layer target icon is filled in, and somtimes not.
Can somone explain to me what the difference is?
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From the Illustrator help pages
The target icon indicates whether an item in the layer hierarchy has any appearance attributes and whether it is targeted
The filled in icon means the layer has appearance attributes beyond a single fill and a single stroke.
You can read more here: https://helpx.adobe.com/illustrator/using/appearance-attributes.html