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 ? AnonymousCanCreateDirs no
Change this to something like LimitRecursion 20000 20 etc.