The pure-ftp daemon by default has a recursion limit of 2000 files, this prevents the server from showing more then 2000 files when you browse a directory with an FTP client. To expand this Limit to e.g 5000 files, create or edit the file /etc/pure-ftpd/conf/LimitRecursion and add a line "5000 500". The first number is the number of files, the second is the max. directory depth.
echo "5000 500" > /etc/pure-ftpd/conf/LimitRecursion
and then restart pureftpd:
service pure-ftpd-mysql restart