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Last week one of my Jira cloud migrations failed because the number of users exceeded the limit of 50 users on the cloud site. There were definitely only 49 licensed users. However, some of those users already existed in the cloud. When migrating from server to cloud it seems that the email address associated with several cloud users was all in lower case, while the email address associated with those same users was in mixed case in Server. For example, John Doe might be email@example.com in the cloud, while in Server the address might have been JohnDoe@example.com.
Does the JCMA/CCMA interpret these as two distinct and different email addresses?
JCMA email check is not case sensitive, so it should see those emails as 1 and not consider them as separate. Were you able to get past this check since you posted the question?
I'm sure you have seen this document before, but here is a reference to how users and groups are migrated with JCMA: https://support.atlassian.com/migration/docs/determine-your-user-migration-strategy/#Migrate-Jira-users-with-the-Jira-Cloud-Migration-Assistant