This can be done with the FTP folder as additional folder in the "COPY FILES" mode.
You should select "Backup mode"="Copy files" and configure main
backup folder to the local drive. Configure local backup folder
without using "date format". And the option "If destination
archive with the same name already exists" = "delete old
Then configure the "Upload to FTP" panel.
In this case first APBackup creates temp local folder with
incremental backup on the local drive (without empty folders) and
then copies this temp folder to FTP server.