I am transitioning away from ArcMap and to Pro but running into a consistent issue. When adding new layers to a map already containing content (other feature layers), the data source of these existing layers becomes changed. In other words, the feature layer will suddenly be referencing some incorrect geodatabase feature class, in some cases of a different geometry type which then prevents me from repairing the data source.
My guess is that this has something to do with the way the ArcPro is indexing or keeping track of layer order. This error/issue has occurred regardless of whether I drag and drop data into the map, use the "Add Data" dialog or if data is added as a result of running a GP tool.
1. Check if rebooting ArcGIS Pro or the machine, helps.
2. Does the issue occur when you create a new project, follow the steps.
If the problem persists, could you describe the steps through which reproduce the issue?
What are the data sources of your existing layers (shapefiles, File GDB, Ent. GDB, etc.)?