The Pharos CA certificate is a file located on the Omega SmartHub at:

/etc/station/PharosCACertificate.crt

This file can be replaced with a new certificate of the same name. Rename the CA certificate you want to use to "PharosCACertificate.crt" and upload it to the SmartHub, either via SCP on port 8022, or using the Files screen in Omega Administrator (this screen is available in 2.1.0 firmware or later). The replacement file must be Base64 encoded.  This is not the default export method from the Microsoft Certificate management snap-in.

Note: You may need the root CA certificate and Intermediate CA certificates (depending on what certificate the EDI server has installed). You should be able to include both in the PharosCACertificate.crt file.
The Microsoft Certificate management snap-in does not allow you to export multiple certificates in Base64 encoding, so you must export them separately, and then concatenate the files (e.g. by opening both files in Notepad, copying the contents of one and pasting at the end of the other).  The order of the certificates in the combined file is not important.