Encryption of a file share that gets populated automatically by a Python batch transfer?

Problem:

We have our SOPHOS Safeguard 6.0 on several desktops. These desktops all have a server file share whose contents we want to have encrypted continuously (so this shared folder information is never in a decrypted state for security reasons).

The issue:

We use a python script to call another server (at night) that automates the population of this file share.

When the Sophos end users open their respective shared drives in the morning the information on these encrypted drives is not  encrypted automatically.

Possible Solutions:

Is there any way using Safeguard in this scenario to make this file share information is encrypted at the time of the server batch transfer?