Is there perhaps a setting that is redirecting Apple Mail given Mojave's new security measures? I spent a few hours with an Apple Senior Tech who could not resolve it. I will hear from Apple Engineers on Wednesday. I am not the only one with this problem though I assume that others might be using Little Snitch as well.
A temporary TEST User did not have this problem. There is therefore a network setting that is causing all new email to vanish from the inbox.
General discussions about Little Snitch
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