Good news everybody, IPv6 support is coming to FileZilla Server.
Unfortunately the support for IP address filters not using CIDR notation will be dropped in the new version. Maintaining the old filter syntax to support both IPv4 as well as IPv6 would be too much effort and way too frail. Affected users will have to redo their address filters using CIDR notation.
The plan is to get the IPv6 enabled version out on time for the world IPv6 day.