We've been using HipChat Server for a year and still have issues with notifications, notification badges for missed chats while offline, and notifications syncing across devices.
Are these issues still present with data center?
Thanks for your query. To answer your question, we're working on fixing this issue in HC Data Center and Server.
Please see this HCPUB suggestion and follow it for updates: https://jira.atlassian.com/browse/HCPUB-2603 We'll update it with progress and early access information as we continue to march towards resolving this.