We are trying to clone a new webmap (not classic) to a different organization and having some issues. The webmap has a mix of grouped layers and a couple of single layers. When we clone the webmap, it only copies over the map and the single layers. Grouped layers doesn't get copied over to the destination AGO and the webmap refers to the layer in the origin AGO.
We tried the classic AGO assistant, AGO assistant beta and the Python API's clone_items() function. It seems none of the methods is able to copy over the grouped layers. We are going to try saving a copy of the map in classic version and cloning then reconfiguring grouping in the destination AGO, but I wanted to ask the community if there's a way to clone the new webmap without losing grouping.
I ran into this issue yesterday as well.
The clone_items function perfectly replicates layers that aren't grouped in the webmap and completely ignores the ones that are and tries to point back to the original. I've logged a support case against it, as I suspect it's a bug...but quite big one!
For the record this was logged as:
BUG-000152758
It has been addressed and is fixed in version 2.1.0 of the ArcGIS API