Is there anyway to increase FTP timeouts (either on the VPs end or the client end)? Newbie here so any detailed info woudl be greatly appreciated. VPS account is using cpanel but cannot seem to find something in here to change this.
You need to set this in the FTP config file. Most likely you are running pure-ftpd, so the conf would be /etc/pure-ftpd.conf. Open it and find a line called "MaxIdleTime", this is set to 15 by default - meaning, 15 minutes.
Once you change it, save the file and restart the ftp server.