I think that when an item is created from an existing feature layer:
# Create a new empty comment layer from the already existing base comment layer
layer_properties={
'title':'Test_Comment_Layer',
'description':'This is a comment layer that is being used for testing purposes only',
'tags':'Test, Python, Comment Layer',
'type':'Feature Service',
'url':'URL HERE'
}
base_comment_layer = gis.content.add(item_properties=layer_properties, data="URL HERE", folder=pf_name)
that we should be able to choose which layers we would like to add from that Hosted Feature Layer (or Feature Layer Collection):
1) Create feature layer from existing layer:

2) Specify layers to include:

The above code will create a Hosted Feature Layer with all layers included.
Correct me if I'm wrong... but I would assume that this could be specified in the item_properties described in the content manager section ArcGIS API for Python guide:
arcgis.gis module — arcgis 1.0.1 documentation
It seems simple to delete features of a layer, or to delete the feature layer collection itself, but to delete a layer that is a part of a feature layer collection (or specify which layers to include) is not an easy task.