When you update your dashboards module to the latest version you should also upgrade your custom dashboard in order to use the latest functionality. Each template references a particular version of the dashboards module code, you can see this at the start of the app.js file.
In order to update your dashboard you should copy any files which you have not changed from the latest version of the template into your dashboard folder in the overrides folder. Then compare the differences and make changes to the files which you have modified (typically app.js where you have added your custom menu items to the adminTemplate).
For the adminTemplate, typically you should copy and overwrite the index.html file, the directives folder, views/login.html, views/dashboard/main.html and views/dashboard/errors.html. Make sure you update the two references to
adminTemplate in index.html to the name of your dashboard folder you created in overrides.
You will need to manually update your app.js and re-insert your menu items. Typically this will be the easiest way as the only thing you will have changed is the menu-items. Here is a diff file showing the differences in app.js which may help you to upgrade - https://gist.github.com/jazdw/8a28f156fa3a39d1712b929be8866248