Does he have any add-ons in Thunderbird that might be interfering here? A cursory search for thunderbird changing reply-to came up with this, for example:
https://addons.thunderbird.net/en-US/thunderbird/addon/stop-ignoring-reply-to/
Also, it might help if you can get the raw email that he receives and maybe having him try a different email client or webmail if available to test.