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If you clone a template for editing and customization, you can see that whenever the original template is upgraded, the cloned template also got the upgrade notification.
Image Added 

If you want to remove this update notification on cloned template, you can do as following:

1. Open file at:

.../PF.Site/flavors/name-of-cloned-template/theme.json

 2. Edit the code and remove a line then save the changes on the file:

{
    "id": "material",
    "name": "Material_cloned",
    "store_id": "2004",     //Remove this line
    "version": "4.6.1p2",
    "vars": {
        "body-bg": {
            "title": "Body Background",
            "id": "body",
            "attr": "background"
        },
......