sean Yes, you're missing the point. Until you switched on the empty mailboxes, I had all my emails still available locally in Thunderbird and in the iOS email app.
Now, they're all gone, because you're presenting the clients with empty folders, and they dutifully clear everything out to sync local with remote. It's safer for there to be no connection at all.
I have someone using one of my mailboxes who is now essentially locked out of her work because if she opens her email client, her essential work-related emails will disappear until the restore operation completes. The outage this morning meant she couldn't receive any new work, but she could at least deliver old work via a different email address. You clearing the mailboxes now means she can't do that old work either.