Hi,
I have allot of experience with running C#/.NET on Ubuntu and Debian using Mono runtime.
From what I understand, you have a C# application, and you want to add code/function to send a zip file to a remote Linux server.
There are multiple ways to do this, HTTP, FTP, file transfer over SSH, .. if you do not have FTP already installed on the remote server, we can use "SSH", which will require almost no modification to the remote server that the files will be copied to, and after transfer, we could check the uploaded files, and verify that it has been uploaded properly.
Looking forward to working with you, and I hope I see some of the source code or get more detailed information before going forward with the project, to have more information about what need to be done.
Thanks.
Hashem.