By default empty parent packages are hidden in the package explorer, if you modify the Filters… in the Package Explorer to uncheck Empty Parent Packages (third from top in second screenshot) you’ll be able to see the empty packages.
(source: eclipse.org)
You can then rename the com package and check the Rename subpackages option to force all child packages to be renamed.
(source: eclipse.org)
Then when you’re done reapply the filter to hide all those empty packages again.