If your ftp-software does not display more than 1998 file names (2000 with symbolic links), you must change config file of Pure-FTP and restart ftpd. Use a ssh-client , recommend Putty.
[ssh] pico -w /etc/pure-ftpd.conf
# 'ls' recursion limits. The first argument is the maximum number of
# files to be displayed. The second one is the max subdirectories depth
LimitRecursion 2000 8
# Are anonymous users allowed to create new directories ?
Change this to something like LimitRecursion 20000 20 etc.
Another solution is change it from command line:
/usr/sbin/pure-ftpd -L 20000:20
If you are using cpanel you could get this error : Unable to start a standalone server: Address already in use
. If you see such outpus try first solution and restart your ftp-server via:
[ssh]# service pure-ftpd restart