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Updating a map workflow

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I have a question regarding the workflow when updating data in ArcGIS.

I have lots of shapefiles in a geodatabase with a couple of different annotations for different maps. When I receive updates I get a new shape-file for the updated layer including all the layers contents, not only the changes. What's the best way of updating my own data with the new?

I know that if I do changes in my shapefiles, the annotations will automatically be updated, but if I'm not exactly sure what's new in the new shape-file I kind of want to replace the data but still keep the locations of all the annotations. How do I do that? Do I have to look up the changes and do them manually in my data?

thank you

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