“Would like to have all the content from his CompanyX account archived (which is not the pickle here) and keep on working with the companyY structure in his mailbox, connected to his regular (AD) user”
Please clarify whether companyX and conpanyY are under the same tenant?
If yes, for the part of the X mailbox, you can first export the content to PST, and then remove the license of X. Then use SMTP matching to associate Y's mailbox with X's AD account.
More detailed steps please refer to: How to use SMTP matching to match on-premises user accounts to Office 365 user accounts for directory synchronization - Microsoft Support
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