The fix I use for this is to change the settings of that particular e-mail
accout to keep messages on the server. That way when you download the
messages from your ISP the messages themselves will not be deleted from your
ISP.
What you can do is change this setting on one computer and leave the other
alone. This way the messages will not remain on your server indefinately.
....or you could change the settings on both computers to leave messages on
the server and check the box to delete the messages off the server 10 days
after it is first downloaded. The second option is the one I use myself.
Neither option is perfect, but it should be better than what you have now.
Hope this helps,
Jeffrey