This issue occurs because of each Microsoft Dynamics CRM deployment will try to synchronize their synchronized items and settings to the same mailbox. Each deployment will compete with one another to update their information on this mailbox. For example, if you have multiple tracked email messages from CRM deployment A, when CRM deployment B synchronizes with the same mailbox by using the settings from deployment B, it may untrack these email messages.
A scenario such as this might have occurred by using the same mailbox for a production CRM deployment and a development deployment. In this case, you would have to remove the configuration for one of the deployments or use a separate mailbox for one of the deployments.