Hi @ TPMR,
I'm glad to hear that the issue had solved and thanks for sharing.
Since the Microsoft Q&A community has a policy that "The question author cannot accept their own answer. They can only accept answers by others.". and according to the scenario introduced here: Answering your own questions on Microsoft Q&A, I would make a brief summary of this thread:
[O365 Sender alias being stripped from emails]
We have a local SMTP relay setup to enable various on-site devices (printers etc.) to send emails.
Mail flow rules are applied based on the headers of received messages. Around 0:00 GMT, suddenly the mail flow rule is not running, and the check header no longer contains the alias used.
No processing, the issue has resolved itself. Expect a temporary issue with the operation of the O365 backend server.
You could click the "Accept Answer" button for this summary to close this thread, and this can make it easier for other community member's to see the useful information when reading this thread. Thanks!