You may not have the best signal on your phone so they are only being deleted and not synchronizing. Try to update your prl by dialing *228 then selecting option 2. This should help resolve your problem. Hope this helps.
Zachary- can you offer any help/timeline with the current opposite problem in these threads ( POP3 emails disappearing since the upgrade) ?
Regarding emails disappearing, this is a response I wrote in a similar thread on this subject:
First of all I want to state that my Froyo upgrade went flawlessly. My phone works fine in every respect with the exception of how 2.2 handles POP email accounts. I want to make 2 points about the 2.2 update and how it handles POP email accounts: First, I really don't think these Verizon techs are even aware of how 2.1 handled POP email accounts so when they see how 2.2 handles them they think there is no problem because in their minds the behavior seems reasonable. Lastly, and this has appeared in other threads on this subject, Verizon has confirmed that the way 2.2 handles POP email accounts is by design and is NOT a bug although many of us, including myself, feel this design is a step backwards and an update to return to 2.1 POP functionality is warranted. I use Outlook as my email client. When Outlook connects to my POP email servers it downloads all emails to a local store (.pst file) on my computer. What I choose to do with the original copies of the emails residing on the server will have no effect and should not have any effect on the copies of the emails saved in my local store. If I configure Outlook to delete the email on the server after it is downloaded the copy still exists in my local store. That is, the state of the POP server (from a content point of view) is NOTmirrored in my local store which is exactly what I want and expect. Prior to the 2.2 update, this was how 2.1 handled POP email accounts. The 2.2 update causes email content on the phone to "mirror" the content on the server; as long as an email resides on the server it will remain on the phone; if an email is deleted from the server it will also get deleted from the phone the next time the email sync's with the server. This is not the behavior that we want or expected to have after the update. This behavior was not listed in the documented feature list of 2.2 although we are being told this was by design. This "behavior" is very easy to replicate. All Verizon needs is a DINC still running 2.1 and a DINC running 2.2. The difference between how POP email accounts are handled between the 2 versions will be obvious if they just try it out. So our message to Verizon is simple; give us a patch that will restore POP email support in 2.2 to the 2.1 functionality OR restore POP support in 2.2 to the 2.1 functionality BUT add an additiional "setting" that will give you the current 2.2 functionality for those who want that sort of behavior. This way everyone is happy (I think). I would think this would be a relatively simple thing to fix. The problem is getting Verizon to acknowledge the the change in functionality between 2.1 and 2.2 and I think that will only happen if enough people complain about it.
I called VZW tech support last night to tell them my phone was still deleting emails and they told me it was a hardware problem and that I could go to the VZW store and exchange for a new one (since I am under the 30 day period). I went to the store today with in mind that this was more or less likely a software problem (2.1 vs 2.2) and that is what the store told me. They confirmed this when we used one of their store models with 2.2 on it and it did the exact same thing. They told me that exchanging the phone really would do nothing because the same problem would happen again. It is because the Droid was not exactly designed around email like a Blackberry. They basically told me that I could exchange for a BB or wait for a fix or an app that works with POP3. I chose to wait because I do not have my phone because of email (though it is nice to know it would work; I am happy with just Gmail).
As for the server delete vs not delete, I had mine checked to not delete but it still deleted. Oh well. I guess I will wait for an update. Gmail will still open the same attachments (though you cannot download them directly to your phone; there is an app for that though). It just will not email though attachments if they are on your SD card (you can forward them though).
I am still happy with the overall performance of the phone (minus POP3 problems).