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Unfortunately I've recovered all my inactive mailboxes recently, so I don't have one handy to test in order to confirm this. Have you tried adding an exception via the SCC UI?
Perhaps TonyRedmond can help here. Or you can just open a support case to get a proper answer.
I don't think inactive mailboxes are processed by the Managed Folder Assistant even when a retention policies covers all mailboxes. These mailboxes are, after all, "inactive." They will be removed from Office 365 after any holds that cover the mailboxes lapse.
In other words, check what organizational and specific holds exist belonging to eDiscovery cases (Office 365 and Exchange) and remove the holds from any inactive mailboxes. For example, the screen shot shows that a number of inactive mailboxes are under hold. The inactive mailboxes are indicated clearly. If you remove any of these mailboxes from the hold - and it is the last hold the mailbox is covered by - it is removed from Office 365.