Hello,
Thanks for reaching out.
Please follow the steps below to ensure that the custom template is not deleted after the plugin update:
1. Copy page-templates or link-templates directory from /plugins/download-manager/src/package/views directory to your active theme directory.
2. Make a new directory as download-manager in your active theme directory.
3. Now remove all files from {active-theme}/download-manager/page-templates or link-templates except the template files you need to update.
4. Update/copy template file(s) in {active-theme}/download-manager/page-templates or link-template directory as per your need.
Note: If you save link/page template by following the mentioned steps it will be deleted after a theme update.
If you have further queries, feel free to ask.
Regards