If you are synchronizing your phone calls and tasks into Exchange/Outlook, then any actions being taken in Outlook could be impacting what is in Dynamics. Example, if tasks and phone calls are synched into Exchange and the user is removing them in Outlook that can cause them to be deleted out of Dynamics. If you are using any automatic exchange archiving tools the movement by the archival tool will have the same effect – any synchronized activities that are visible in Outlook that are moved to an online archive appear to Dynamics as having been deleted and therefore the synchronization back to Dynamics will interpret this as a delete and remove from Dynamics. Fun times.
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