Here's your person. It just happened to me again. I've had the ipad for 2 years and its done it to me 3 times now. I also have POP, have talked to my provider, checked all my settings. Everything is as it should be. Did u ever find a solution?
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 my 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. The email app did lock up briefly at the same time.
I've been combing the forums for help. Seems like many have this problem, but no solutions. My thoughts on what people say about pop3 mail, bs! I've been using it all this time on two pcs and the iPhone with zero issues until now. And it's absurd that iPhone/ipad backups do not include email messages.
I'm going to meet with one of the apple 'geniuses' and see if they can help. I'll post any solutions.