The Architecture Design of Cloud service is different then App Service. Cloud Service is hosted on its own dedicated environment. Cloud Service is NOT hosted on Shared Server like App Service.
When you create package for the Cloud Service. it contains all information of it's roles, Size of roles, number of instances per role and what files needs to be hosted on that role. ( Other information also).
if you have multiple roles in your cloud service. there will be dedicated VM for each instance of the Role. so your files will be placed on each role of that VM.
if you want to change any file from the deployment, you need to change it on all instances.
Remember that if you restart the Cloud Service or Role all changes made in the file will be lost. Cloud Service will restore the old files. ( files at the time of deployment).
you can enable the remote login for roles and check the files.
if you want to know more about cloud Service check : http://avipatils.blogspot.in/