Email Deletes After iTunes Sync, WHY!!?? 3GS OS 3.1.3

Why does my email in my POP3 account inbox delete after/during sync with iTunes?

It shouldn't. Email account mailboxes and messages are not included with the iTunes sync process.
Do you have the email account selected under the Info tab for your iPhone sync preferences with iTunes to transfer the email account settings from your computer to your iPhone? If so, this only needs to be done once and can be deselected after the email account settings are successfully transferred to your iPhone.
If selected, deselect this followed by selecting apply to see if this makes any difference.

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