C#. Security and Efficiency Loopholes When Uploading Files through a .Net Application via SFTP

I need advice from developers who have either faced or have experience dealing with a situation similar to the one described below; just to avoid reinventing the wheel.

Situation:

We have a C# Winform application running at multiple sites (100+) where each site generate an average of 30 new data files per week varying in sizes from 10-40 MB per file. We want to maintain a data store for all data generated in the field using a one-way synch. It is a medical application hence the security of this data during transmission is extremely important.

Our Solution:

Since all new data is created in new files, we think that a diff based data replication system (such as rsync) is NOT essential. Instead, we are writing a custom application that runs in the background as a Windows service and uses an SFTP.Net wrapper (chilkat) to upload new data files to our Linux server at regular intervals. Data from each site is uploaded to a separate pre-configured folder on the server. Our custom client application keeps track of which files it has uploaded in a local SQLlite database. The Chilkat API allows us to authenticate using username/password or keys.

Questions:

1. Would you consider above solution to be prone to security flaws with respect to data transmission?

2. Would you have effeciency concerns with our approach?

3. Are there any better alternatives than what we are proposing. Our client machine are Windows and the 开发者_开发技巧server is Linux based (we can move to a Windows server too, but that is certainly not a prefernce.)

Thanks in advance....

m.umer