You can execute this from RootDirectoryI (it is essential that you run it from RootDirectoryI):
cp--parents-r*/Subfolder1../RootDirectoryII
This works by copying (-r lets you copy entire directories) each Subfolder1 that exists in second level nesting to RootDirectoryII.
The --parents option copies the path used to get to the copied file, so in this example, it makes each Subfolder1 reside not right under RootDirecoryII but nested under a Folder*, like it was in the first place