I have been having the same issues. I have two pop3 email accounts and are both set up correctly. No issues at all on my iPhone, but on my gen 3 ipad every once in a while messages in my inbox just go missing. Seems to happen when starting a manual download of 100 plus messages (mostly spam!). And yes, I have settings at displaying 400 messages. This is incredibly frustrating and can't depend on the main function of this device.
So to be clear on the issue, it's a pop3 mail account (both of them), set to leave on the server after download, fetch was turned off but I'm trying it on now. This has happened multiple times and happened again last night. Started downloading about 120 messages and then all inbox messages older than about 3 days just disappear. Other times it was all messages that were gone.
I've been combing the forums for help. Seems like many have this problem, but no solutions. I'm going to meet with one of the apple 'geniuses' and see if they can help. I'll post any solutions.
I have been having this issue since I got my ipad at Christmas. I too have trauled the web looking for a solution and had found none. Actually it's quite simple. You have to go into settings, default account, and then select the account that the mails are disappearing from and as long as you haven't deleted them from the server on this account they will reappear in your inbox as if by magic! Ipad automatically selects your me account so if this is not the one you generally use then messages will disappear. The downside, if that's what to call it is that all sent messages will also go from this default account so it must be managed properly. Hope this helps all you other poor souls who've been having the same problem!
A simply solution is set up a gmail account and forward all mail to that account. First spam filter is the best and it works very efficiently
I have 5 different accounts and have minimum issues. I would never recommend hot mail to any user. On my devices I use mailbox as the email client again offers more features than mail. Hopefully ios7 will offer improvements for mail.
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