Description
Web scene layers can be published from scene layer packages or from referenced scene caches in folder or cloud data stores. The target layer and update layer must be published in the same method. For example, if the target layer is a web scene layer published from a scene layer package, the update layer must also be a web scene layer published from a scene layer package. You cannot replace a web scene layer published from a scene layer package with a web scene layer published from a referenced scene cache.
Solution
Publish the update layer in the same way that you published the target layer.
See Replace a web scene layer for more information.