This file exists in 5.6.1 but after installing 6.0.0 on Ubuntu 16.04 .... it does not exist anymore.
That is correct. We no longer use this file in 6.0.0.
The core issue you have is that your elasticsearch.service
file still refers to it (although you've since resolved that).
It is likely that you edited that elasticsearch.service
at some point in the past, so when you upgraded your elasticsearch install, the package manager was unable to reconcile the changes in the .deb with your local installation.
Even though you have worked around this issue, you should check the logs from your upgrade because it is possible that you have missed other installation steps that could be important.
Please see the first half of this thread: