This has happened twice now (ArcGIS desktop 10.4.1) in unrelated projects with different data:
General steps:
I have been using ArcGIS online since it first came out, and I have never seen anything like it. The only work around I could find was to delete my feature service and publish a new one.
Has anyone else had this problem? Perhaps this was addressed in the 10.5 update?
Thanks
HI Dan,
Are you shifting the order of your layers when you overwrite the service? If so, it sounds like the underlying data has shifted, while the web map is still expecting the old layer order.
The layers in the web map are operational layers in the web map specification. If the order of layers has changed in the feature service, the web map may not be aware. If you think this is what is causing the issue, try to add new layers to the bottom of your map document when overwriting services.
If this doesn't sound like the cause of the issue, I suggest contacting Esri Support Services.
-Kelly
I had this same thing happen recently, and I determined it was because I had inserted a new layer in between existing layers the TOC of the Service .mxd after my initial publish. When I re-published, it messed up the symbology.
Since REST service endpoints use numeric identifiers for each layer in the feature service (i.e....arcgis/rest/services/Temp/Temp_Mburg_Schools_TEMP/FeatureServer/0, or arcgis/rest/services/Temp/Temp_Mburg_Schools_TEMP/FeatureServer/1), the numbering was thrown off by the insertion of a new numeric identifier. The Service definition uses the numeric identifier to draw the symbol, but it still thinks that layer/1 is schools when it's now police stations. Now, police stations are symbolized with the school symbol. Thus, all layers below the new layer I have inserted has incorrect symbology.
The only way I was able to fix it was to remove the Service from the web map and re-add it. No problems after that. Kelly's idea to only add layers to the bottom of the TOC in the .mxd prevents this from happening, but sometimes I want layers in a specific order, hence the need to delete the Service and add it again to the web map. The problem with doing that is that popups must be reconfigured again after adding the service back in.
I know this is an old post, but I just ran into this so wanted to share my workaround.
~also Kelly