That repository is a system repository and shouldn’t be removed. I suggest you restore the file, especially if you find that Store doesn’t work properly. Generally speaking, only the user-added repos should be removed or disabled; see ssu lr output. store is listed on the user repositories, but it’s “built-in” and points to a Jolla domain.
Also, there has been some “stickyness” with the update notification in some cases - in this case manually checking for updates in Settings should fix the notification.