Pop-ups for feature layers in a web map are switched after overwriting a feature service using an MXD where the layers order changed or has another layer added that changes the order of layers.
Last Published: August 21, 2015ArcGIS Online
Bug ID Number
August 20, 2015
August 21, 2020
After review by the development team, it has been determined that this issue is related to a known limitation with the software that lies outside of Esri's control. The issue's Additional Information section may contain further explanation.
This is addressed by the following setting introduced in ArcGIS Server 10.3.
This is a known behavior of services. ArcGIS Server 10.3 introduced a setting to address this behavior.
Follow the instructions below to workaround this issue:
1. Open the .mxd.
2. Do not add a new layer or shuffle layers order.
3. Open the data frame’s property page.
4. Enable ‘Allow assignment of unique numeric IDs for map service publishing’.
Note: This should assign a unique ID to all layers automatically. The numbers should be in sequential order (similar to map service). Depending on the version, with group layers or annotation layers, the numbers may not be exactly in sequence and may not match with what have been reported in map service REST end point. If that happens, manually open all of those layers property pages and update layer IDs to match with map service’s.
5. Add a new layer (or change layer order).
6. Publish to override the existing map service.
For more information, refer to http://server.arcgis.com/en/server/10.3/publish-services/windows/map-authoring-considerations.htm#ESRI_SECTION1_4C54586DEB0445B4B97AF15856E546AB