The number one thing to realize ahead of time in the "We're moving to cloud and we have Jira Align" scenario, is that the issue IDs from your source Jira instance need to remain the same in the target instance, otherwise you could end up with a pile of unwanted issues, literally and figuratively. I've had a Jira Align client in the past who migrated their on-prem Jira instance to Cloud, didn't notify anyone including Atlassian, and it ended up a hairy mess that required a lot of extra elbow-grease to fix. While migrating, they didn’t keep the issue IDs consistent across Jira instances, causing Jira Align to have duplicate upon duplicate. Fixing mass duplicates in Jira Align requires something close to intensive surgery, so it’s important to try and do everything possible to prevent this problem. Rich Sparks from the Jira Align team at Atlassian comments on this topic further in this community article.
The connector for Jira Cloud and Jira Align will soon be updated and should alleviate a good portion of administrative pain with regards to mapping sprints and boards. This Atlassian community article speaks broadly to those pains and their plans to address them. In general, I'm counting on the integration between Jira Align and Jira Cloud to be better than with Jira on-prem, and am looking forward to more proof in the pudding on that soon.
I’ve not seen this yet pop up on the Jira Align roadmap, however given that Atlassian is keen on supporting their Enterprise clients at scale with their cloud-first approach, I’d be surprised if it doesn’t show up for a future release one day.
There was previously a bug that caused users to become duplicated in Jira Align if the user didn't check a particular setting in their user profile prior to migrating. Atlassian has fixed that bug, and it's a good thing too, because there's currently no good fix if it does occur. I was relieved to see that with a recent client implementation, we didn’t see this issue pop up at all.
Here is the official Atlassian article, and here is an unofficial blurb on the topic:
...for some of the integrated user accounts you will see hashed/encrypted email addresses if the user didn’t make their email address visible to anyone. There was a solution implemented in the connector to resolve this from happening but it could be that it doesn't resolve it a 100% of the time. You may see a duplicate user account when a full user’s email address comes across as encrypted when they're assigned an issue in Jira that syncs with Jira Align. Jira Align compares the email address from the Jira user account to match it to an existing Jira Align account. When the email address is encrypted it may result in duplicate user accounts. Again this is not 100% of the cases due to a solution that was implemented to resolve this issue.
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