@DavidPike
Do you have static ids assigned to layers/tables in the source mxd?
Here is the link to the help topic to find more info on that: https://pro.arcgis.com/en/pro-app/latest/help/sharing/overview/introduction-to-sharing-web-layers.ht...
If not, I'd highly recommend you to do that? It is supported both in ArcGIS Pro and ArcMap.Once you turn this option on, double check to make sure layer/table ids matched with what you have in the service REST end point. In case you see any discrepancies, you can update that in layer/table properties page before updating your map service.
This will make sure once you update your map service with layers, all your webmaps and app will continue to work.
Only thing is that the new layers might not appear in your existing webmaps in some cases e.g. if you reordered sublayers inside the map image layer, or updated their symbology etc. And at that point, you might need to manually insert the new layer definition in the webmap json. That said, I'm not an expert in webmap area, there might be other easier way to do that.
Hope you will find this helpful.
