When you add a layer to a service, the webmap does not see it. Until you re-add the layer. We have to redo all popups, labels, symbology, other webmap settings etc. Stressful for production viewers.
First, ideally the issue of webmap staying in sync with services will be resolved in an AGOL update.
So re-adding it will become unnecessary. (in other words we shouldn't need to constantly re-add a service to a webmap just because we add or remove layers in the MXD)
But the connected issue to this, is it changes the 'id' of the service 'layer' in the webmap JSON, if you re-add a service. This needs to remain static or at least have some way of us being able to arbitrarily set it, so I can change it back to what it was. Or perhaps (and in addition to, as an optional alternative) reference the layer by 'name' as I proposed last year.
The reason the 'id' is so, so important is it is vital to how the Share widget in webApp Builder works, and how we can programmatically do things like expand layers in the layer list or do other actions. Because this 'id' gets carried into the DOM node IDs.
From my earlier thread....
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