Hi @JustinMicheal-7973 ,
Based on my knowledge, we could not make inactive mailboxes by removing licenses.
Here are two steps to make a mailbox inactive: 1) placing the mailbox on Litigation Hold or applying a retention policy to it, and 2) deleting the mailbox or corresponding user account. Above is mentioned in the official blog for your reference: Create an inactive mailbox
For further troubleshooting, How do you delete the exchange online mailbox? Comparing the detailed steps with the blog and check if there something wrong with your steps.
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