The JiraProvisioner may be configured with a Group Identifier Type. "If selected, only groups with this identifier type will be provisioned." Further, Group Name From Identifier can be ticked/checked, so that the provisioner will "Use the value of the identifier as the name of group in Jira".

The problem is that if you create a new CO Group with the same name as an existing group in Jira, it does not have the Identifier yet in COmanage, and so the provisioner will delete the existing group in Jira.