I am going to guess you are using IMAP, but the settings should be the same for both IMAP and POP in outlook2007 (if I remember correctly).
You might want to disconnect your machine from the internet to avoid it moving more mail to the trash
In outlook goto
Tools, Accounts and highlight the account you are having issues with. Select the "change" button.
Click "More settings", then click the Advanced tab.
Place a checkmark in "Leave a copy of messages on server"
Uncheck both of the "remove" options below that.
Click OK and close outlook, go back online and see if it fixes the issue.