Disappearing mail in INBOX

I use Earthlink for my ISP. If I read my emails on Earthlink's Web Mail and then open my Apple Mail app my Inbox will appear empty. It seems that any email I opened in Earthlink will disappear in Mail along with all emails received earlier.
Why would this happen? My email situation is a mess because of this.
The emails are not lost; they still reside on the harddrive. Apple's Mail just won't load them into the Inbox.
On other occassions the mail will reappear in the Inbox. I haven't pinned down the mechanism yet but it may be that mail reappears if I don't use my ISP's Web Mail for a couple of rounds.

Cracked it myself, after a bit of thinking. I was using a mail rule moving non spam to my main in box from the IMAP box when downloading, so when iphone looked only spam was left. If mac uploaded the mail and moved after the iPhone, the non spam disappeared. By changing the rule to copy instead of move seems to have solved all the issues.

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