Ubuntu – Configure FTP Server with two different IP addresses on different subnets and separate NICs

The FTP protocol was created when all machines on the internet were globally addressable with a unique IP address. The only reason FTP behind a NAT appliances works now is because the NAT appliance filters FTP traffic and corrects the clear text of the FTP command connection (port 21) to allow for the non-routable addresses involved.

Since you're wrapping your FTP traffic in SSL the NAT appliance cannot read this traffic and so cannot correct for your non-compliant IP addressing. Your solution is going to come from your FTP server.

pure-ftpd has an -N flag that forces "active" mode meaning the FTP server initiates the data transfer (port 20) and will refuse "passive" mode. Passive mode is what FTP clients behind NAT have to use to download from a public FTP site, which you will no longer be compatible with.

proftpd (the best of all posible FTP servers that I've bothered to play with) has a config hack to solve this problem. You can add the "MasqueradeAddress xxx.xxx.xxx.xxx" directive to the config file which will make proftpd tell all clients that the MasqueradeAddress is the ip address of the FTP server. Ensure you have port 20 on this address forwarded with NAT to your FTP server.

As per your note: The "MasqueradeAddress" directive can be used in side the scope of the "VirtualHost" directive, allowing you to provide both the inside access as well as the outside NAT access.

I am not fully sure what you are trying to achieve. I can see two possibilities:

1. You have TWO subnets with router in between and want to have ONE DHCP server responsible for IP address assignement. In this case you likely should have a look at dhcprelay (which is also a part of isc-dhcp) or so called "ip helper" or "dhcp helper" on a switch / router.
2. You want two SHARE single physical network segment between TWO subnets. In this case you have to put both subnets in shared-network statement.