SSH as root

cp /etc/pure-ftpd.conf /etc/pure-ftpd.conf-ori1
nano /etc/pure-ftpd.conf

find "LimitRecursion"
You will see this:
LimitRecursion 2000 8

The first number is the limit of files that can be upload.

The second humber is max subdirectories depth.

Restart with this command
service pure-ftp restart