In this case, I was presented with the symptom of meetings disappearing from a Resource mailbox in Exchange 2003 that had been set up for automatic booking with the Exchange 2003 Auto Accept Agent.
After going round and round with the customer to try and get good tracing information from the server, we finally got a good store trace of the behavior.
What was found was that there was a Delegate defined on the Resource Mailbox. Mixing delegates with the Auto Accept Agent can potentially end up causing issues if we're not sure to take precautions. This was the case here.
Note this excerpt from the Auto Accept Agent Deployment and Administration Guide, Managing Resource Mailboxes topic (http://technet.microsoft.com/en-us/library/bb124314(EXCHG.65).aspx):
Modifying Delegate Settings:
You can add delegates to a resource mailbox who can then access the mailbox directly to check existing appointments, check mail in the Inbox, or processed requests in the Sent Items folder. However, if you allow delegates to receive copies of meeting requests sent to a resource mailbox, it is possible that the delegate may accept a meeting request even though the agent has declined the meeting. To avoid this situation, it is recommended that you do not allow delegates to receive copies of meeting requests. You must open the resource mailbox as the primary mailbox to modify delegate settings. You cannot modify delegate settings if the resource mailbox is a secondary mailbox.
To prevent delegates from receiving copies of meeting requests:
1. In Outlook 2003, click Tools and then click Options.
2. On the Delegates tab, select a delegate, and then click Permissions.
3. Clear the check box for Delegate receives copies of meeting-related messages sent to me.
What I saw in our store traces, is that for the problems, the delegates were causing modifications to the calendar. What was likely happening is that the delegate was deleting the copy of the meeting invitation they received, and this in turn was deleting the meeting from the calendar.
We then found that the resource mailbox was indeed set to forward the meeting request copies to the delegates and turned that option off.
After this there was a thought by one user that a meeting disappeared, but additional logging and investigation showed that meeting to have been one that was removed prior to the change in the setting.