Hi,
You wrote: "I have aws set up so that manual update can be used (customer prefers this method). "
I understand that some customers want to be able to manually update the stats, but this does not mean that you should not use automatic updates. No doubt that the stats should be automatically updated every day. Even so, you can allow customers to manually update when they want kind of real time stats.
Now about your question: "How does my customer re-establish stats for the missing days? "
This can be done, but this will be time consuming, because AWStats cannot update the missing days while newer data are already in its database files. So you will have to re-run all the updates for the months with missing days after you have temporarily moved the existing AWStats database files to another directory (to make AWStats believe no newer data is in the database). This requires that the log files for all the passed days of the month are still available.
If you have a different log file for each day, you will have to run these updates specifying the exact file to use for each update. This can be done in the command line with the -LogFile=… option.
This special update process is obviously too complicated for many webmasters. That is why one should not rely on webmasters cllicking daily on the "update now" button.
If you wish, we can also connect to your site to help you update all your clients stats for the missing days for a small fee. Send me a private message if you are interested.