Re: If you are using the Post Office Protocol to keep mail on the server indefinitely, then you are in fact abusing the protocol
In 1996, it probably wasn't common to access a mail account from multiple devices.
People would have a "computer at the office" (Northgate or Gateway 2000, remember those?) running maybe ccMail hooked up primarily to their office mail system.
And all that...
Things have progressed since then.
Still - I agree that POP3 starts being a burden once you get to too many messages, at least used naively (as most desktop mail apps do).
That's why Google came up with "recent" model for Gmail's POP3, and their server, in fact, defaults to "report each message over POP3 once and only once" (which would be seen as "old messages disappearing from server").
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iOS9 -- What? Are you trying to tell me I'm not the only person in the world who has bugs in his code?