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how are these messages being sent? From an authenticated user? or did it work before?
If its from an authenticated user, that is expected as Exchange will resolve that and the alias wont show up in the header.
By the way, have you enabled the ability to send from any alias in Exchange Online? that should preserve the original sender if you can move the mailbox to Exchange Online
https://techcommunity.microsoft.com/t5/exchange-team-blog/sending-from-email-aliases-public-preview/ba-p/3070501
Messages sent to aliases were rewritten to the primary SMTP address in the past. Complex routing configurations may rely on this behavior. When the sending from aliases feature is enabled, rewriting to the user’s primary SMTP address will stop, which could break routing.
When using the user’s primary SMTP address in a Message Trace query, the results do not include messages sent using an alias. To trace messages sent to or from an alias, you need to use the alias in your query. This is less of a known issue and more about highlighting the change to existing behavior.
This feature is for Exchange Online-hosted mailboxes only. Messages to and from on-premises can be subject to rewriting the aliases on those servers.