I’ve had a recent issue of e-mail in my Apple Mail program disappearing (Sierra). By chance I discovered why it did that. I had been so grieved - and Apple’s Tech Support was steering me toward deleting all my mail accounts and setting them all up again (horrors!) - that I want to share it with you in case it will keep anyone else from the same anxiety.
It’s all about Command-L. When you use this command repeatedly it toggles on and off a filter of some kind (that Apple apparently built into the application, as I didn’t set it up) and it makes all the read mail in the mailbox disappear. Unread mail remains. Thankfully I figured this out before said account deletions occurred. :) Doesn’t seem to happen in the “main” mailbox. But I have in-boxes and “Sent” boxes for different e-mail accounts and it occurs in all those.
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