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

The dashboards v3.2 module has functionality to create custom pages and add them to the menu structure directly from the web interface, you may wish to just copy the content of your .html file pages into a custom page. This will avoid the need to manipulate files in the future but will not be a suitable option for people who need advanced pages with their own JavaScript.