Do you have control over file changes? The easiest way to do this is with something event-driven, where a file upload script immediately calls your database updater. Short of that, you can set up a cron job to check each directory for files modified on or after your last check (-m $path >= $timestamp), then process the resulting matches.

As for exporting your data, you can do the usual select and print, or if you need to back up the entire database, you might want to look at mysqldump:

http://dev.mysql.com/doc/mysql/en/mysqldump.html