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From an issue with buffer overlaps, there was this weird problem occurring with an intersect not matching up with the buffers in ArcGIS Pro as shown below:

enter image description here

Upon opening the same exact buffer, with same layer coordinate system, same buffer width, buffer source points, etc. I found that the two softwares were viewing them different as shown below:

enter image description here

In the image above, the buffers were loaded into ArcMap 10.3 (left) and ArcGIS Pro (right). Why is this happening? All of the properties of the layers are exactly identical, but there are clearly some discrepancies. How can I fix this?

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Thanks to Chris W., we were able to find a solution to the problem. In ArcGIS Pro, the coordinate system in ArcGIS Pro for scenes does not initially conform to the layer coordinate system as it does in ArcGIS for Desktop. In ArcGIS Pro you have to specify a coordinate system manually. When a new map or scene is created, the default coordinate system is WGS 1984 Web Mercator. For a global scene, the coordinate system can't be changed. You can choose a different coordinate system for maps and local scenes. I was in a local scene, but I had not adjusted the map default from WGS 1984 Web Mercator. This was set because I initially started the scene as a global scene and then switched it over to local.

I hope that this helps anyone else who runs into the same issue using ArcGIS Pro, and the credit for this solution belongs to Chris W. for the solution in a different thread that got off topic from the original question. The original question can be found here, and has been edited back to the original focus. This can be used if you want a little bit more background information on the topic that lead to the follow up question addressed here.

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