Ashok --
You cannot save a master project with its subprojects as a enterprise project template. This is simply not possible in Project Online. Although the system WILL allow you to save the master project as an enterprise template, it WILL NOT include the subprojects
as part of the template, as you now know.
Because of this limitation, you will need to save each subproject as its own enterprise project template, but you WILL NOT be able to save the external links to other subprojects. Each time you want to create a new master project, you will need to create
each of the individual subprojects from their project template, then create the master project and set the links.
I realize this is a bit of work, but it is simply how the system works. Sorry for the bad news. Hope this helps.