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i believe an additional solution would be to create a topology for the two datasets with rules like polygons must not overlap or must not have dangles/slivers etc. Then run your topology tool bar and your returned results will show each and every place the topology is incorrect. You would then manually go in and merge the errors into a the correct shape.


Take a look at the Integrate (Data Management) tool. Input your shape files, choose a good tolerance, and run the tool. Be aware that it modifies the input data, so perhaps create some copies of your files to work with. Good luck!

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