If you have setup an email account in your email client as a POP account, when your email client is accessing the email it is downloading a copy to your local computer. Once it is downloaded to your computer it will not be visible in your webmail or on your mobile phone. Most email clients will allow you to connect and leave a copy of the email on the server. This setting can be set within the advanced settings of most email clients, and you'll want to enable this setting if using both a POP account and an IMAP account.
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