I have been using this program for my Pocket PC called FlexMail - it is just your standard Pop e-mail program, but it worked better than the one that came with it. I was noticing that when I deleted emails off my Pocket PC it wouldn't delete them from the server right away. So, I changed some of the settings, and I (very stupidly) unchecked the 'Leave a copy of messages on server" button . I thought it wouldn't take the current ones off, . After I did that, I resynced it and it deleted every one of my emails off my Yahoo account! argh! is there a way to recover these? or is there some sort of 'back door' with yahoo where they have a secondary server or something? I thought they would go to the trash folder, but they weren't there.

I seriously doubt Yahoo will restore your free email account from backups. And there's no way to put mail back onto a POP server other than to re-email it. You could send all your messages back out via a redirector. That will send the messages back to your email account without modifying the messages at all, including the envelopes. Mail servers along the way will modify them, but only to add headers you largely don't care about. The only problem with this is that the arrival time of the emails will be now. If you sort them by sent time, which may or may not already be your default, they should look exactly the same. Of course, they have to make it through Yahoo's spam filter, which might be a problem with the dates as off as they're likely to be.

Mail Redirector provides this feature as an extension to Thunderbird.

I assume you just mean for next time if it happens again. but is there a way to retrieve them now? I am sure there isn't but I thought maybe there might be....

I was under the impression you had a copy of the relevant emails on your Pocket PC. If not, the only thing you can do is contact Yahoo. I doubt they're going to be very helpful, though.