Layer ordering is not sequential as expected when publishing a brand new group layer after overwriting an existing group layer with modified ordering.

Workaround

In the ArcGIS Pro map properties, check on the option to allow the assignment of unique numeric IDs for sharing web layers, then click OK. Then, either manually change the layer IDs or reopen those properties and turn that setting back off. Either way, the layer IDs are going to be either what is desired or sequential.

Steps to Reproduce