Hi
with above-suggested options changes will not be overridden in the files .
Beside it, the template update contains new optimize codes , Bug fixes ,and it overrides on the default files .
You can compare the files changes via JA Extension manager Compare option when u are updating the template .
I want to assign a new name for preventing those issue, How can I do it?
Could you explain what do u mean by assign new theme ? If you want to make a duplicate template , it will no more be listed under JA Products and not updated via JAEM , you need to update the template manually by replacing the code .