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I deleted all messages from my mail with mailx d MSGS, and now mailx shows no mail.

But why does cat ~/mbox still show all of the supposedly deleted messages?

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What version of mailx are you using ? What UNIX/Linux OS are you using ? There are mailx variants.... what is your OS, that might help as well.

Note that I found this in the man page of mailx, not sure this is the issue you are encountering, because afaics, the mailx variant of this man page does not accept the d switch on the command line, I might be mistaken, though.

Deletion causes the mailx program to forget about the message. This is not irreversible;

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