OK, you don't want to expose the file contents, with files to be exchanged between three parties, to anyone else.
There are two things to consider:
1) Protect the transport. Here, the files are sent over an encrypted link. So, you're basically putting the normal bits into a tunnel that is encrypted to protect anyone from snooping over the link. This is usually done using SFTP for company-to-company communications and keys are exchanged and authenticated out-of-band before any transfers occur.
2) Protect the files. Here, each file is encrypted independently and then transported to the destination. You encrypt the files of the file before they leave your network and then they are decrypted once they arrive at their destination. This is usually done using PGP for company-to-company communications and the PGP keys are exchanged and authenticated out-of-band before any transfers occur.
If you protect the transport, you're just sending the data through a protected pipe, linking the companies. Once the file is received, it's not encrypted (it's only encrypted through the pipe). If you protect the file, you are block-encrypting files themselves, so it's more of a process to encrypt and decrypt the files; only the actual process/system that has the PGP keys at the receiving end can decrypt the file.
So, what do you want to do? That's a risk decision. If you're only concerned about someone intercepting the file contents that is not company A or B (or C), you need to protect the transport (SFTP, et al). If you're concerned about protecting each file independently and making sure that only specific processes at the receiving end can decrypt the file, you want to protect the files. If the data is very sensitive, and under high risk, you may want to do both.