The below Esri docs show that it is possible to manually set service indices from the source mxd/ArcGIS Pro project:
https://desktop.arcgis.com/en/arcmap/latest/map/publish-map-services/map-authoring-considerations.ht...
Problem: Pop-ups for feature layers in a web map are switched after overwriting a feature service
https://support.esri.com/en/technical-article/000016891
