Agent timeout on Domino server causes loss of document

My project runs a Java agent that creates a log document (does not use the Notes logging facility) in the agent’s database and saves the document every time a write is made to it. However, it appears that when the agent is terminated on the server because it exceeds the allocated time (300 seconds) the document is no longer in the database. Does Domino delete the document if the agent is terminated by the agent manager? I would think that once the document is saved it would be there regardless. The server is running Domino 6.5.4 (not sure of the FPx level). Any comments?

Thanks in advance.