K9 Mail took care of all my POP mail sync issues and then some!
I had considered downloading K9 from the market on several occasions but I didn't after some of the reviews spoke of battery drain, not playing well with the Bionic and some of the screen-shots looked a little cheesey.
I finally got K9 from the market and I could kick myself for not doing this sooner. I really like this program as it solved all my POP issues. My Old D1 would sync up my pop accounts and remove from my phone any email that my pc had already removed, K9 does the same. I was told by many people that I would need IMAP mail to make this happen, well K9 does it just fine.
I also found K9 is packed with features that you don't get on the stock email client like setting mail preview lines, showing each mail account size on my phone, lots of display options and so many more it will take a week to figure this all out.
I am using K9 on my 5 pop accounts and I am still using the Bionic mail for my Exchange account for work as this works well with my work "push"account. I also read that K9 does not yet support Outlook 2010.
I usually do not go on about an app but this one far exceeded my expectations.The best part is it is Free. If you are having pop issues I would suggest giving it a try. K9 may not work for everyone but I was so happy the last couple of mornings when I fired up my phone and the emails I deleted from the PC had also been removed from my phone.