[Darkjedi]

if you don't want it to delete off the server you need to switch to POP email. On the stock ROM you must've selected POP while setting up your email. IMAP is created so that all clients are able to access and edit one consolidated source for emails. Meaning if you move stuff around on your phone, it'll reflect on the server. POP is only a one way stream, where it basically creates a copy of the message and haves you download it, not affecting the actual server. Some POP servers only allow you to download the messages once, after which it disappears from their end.

I run IMAP for the sole reason that I'm able to delete stuff and move emails between folders on my phone and have it reflect on my gmail online.