Actually, I already typed most of them, but didn't post them because I was hoping they were not needed. Since you kindly don't wan't me typing even more
I'll just paste them here. There might be a bit of redundancy with my earlier post.
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If you are stuck with POP3 mail, then my only suggestion is a bit more drastic.
POP3 only allows you two download modes. One downloads your email, but keeps it on the server. The second downloads your email, then deletes it from the server.
If you've been doing the first, then all it takes for all you email to come back as unread is for the iPad to forget what emails it's already seen. If the second, then once the email is downloaded it's gone from anywhere but the iPad. The iPad defaults to the first method. You have to dig around in the accounts advanced settings to change it.
So, my drastic
one-time solutions is to delete your account from the iPad, then add it again. If it clears things up, then the emails were not on the server and you can go on from there. If the emails come back, then you need to do it again, but this time when you set up the account make sure you choose the 'delete after download' option. Once all the emails show up again, you'll have to delete the account and add it yet another time.
If you have another method of accessing the account, say a computer of a website, then you can try the deleting there first, instead of adding and deleting the iPad's account multiple times.
Make sure you've done whatever you need to do with any new emails before you try this. There won't be any getting them back.