For some reason, the proFTP configuration in Virtualmin (v3.88) was not allowing files to be overwritten, despite the configuration in /etc/proftpd/proftpd.conf as follows:
# Umask 022 is a good standard umask to prevent new files and dirs
# (second parm) from being group and world writable.
Umask 022 022
# Normally, we want files to be overwriteable.
# Uncomment this if you are using NIS or LDAP via NSS to retrieve passwords:
# PersistentPasswd off
To solve this, add the following to the bottom of the config file (/etc/proftpd/proftpd.conf):
Then restart proFTP:
service proftpd restart