If you use both machines regularly, but one is the roaming machine and the other is the home machine: only let the home machine actually delete the email after download. So when you're out and about, your laptop will download everything and maintain its own pointers, but not delete stuff from your ISP. When you get home, your main computer will download everything again when you first download it, then delete it from the server. It may work for you, it does for me (phone + laptop + desktop).
This way, your home machine always has everything, and your laptop will have most things.
It's a tickbox somewhere, it's not hard to do.