It is possible to insert / update / delete features in a hosted feature layer. This hosted feature layer can be referenced in a Web Scene.

I believe it is not possible to do this for a scene layer, as I think it is a not supported action. I think to update a scene layer, you will need to create a new scene layer package and use that to wite a new scene layer. Then it is possible to update the excisting scene layer with the new published scene layer. ​@birgit ?

FME currently does not have native tools to do this, but it can be done via Python which can be executed using the PythonCaller combined with web requests executede by HTTPCallers.

There are some new capabilities in ArcGIS Online that allow you to publish a scene layer with a corresponding Feature Layer, you can then use the Feature Layer to update the contents of your scene layer. I think it's pretty new and I don't know if it is even supported in ArcGIS Enterprise. 

How I do it is just publish a new temporary Scene layer and replace your old one using the replaceService command in a HttpCaller. Then throw away the archived (i.e. old version) service away.

I am currently doing the job using Python API. I was wonder if somebody uses FME for the mentioned activity. There is partial caching capability in Enterprise instead of replacing the whole scene layer.