If you go to your inbox, click menu, tools, and options.
What you should do is switch your gmail into an IMAP service, which updates your mail server side as well, i.e. if you delete mail or move it to another folder on your phone, it will reflect on your gmail.com.
In order to set that up you have to add your email address as something like
sovrce@g.com, so it doesn't automatically try to find server settings. Once you select custom/manual set up type in imap.gmail.com for incoming mail server and IMAP4 as account type. Use your gmail username with the @gmail.com at the end and smtp.gmail.com for outgoing mail, while clicking both check boxes for authentication. Under advanced server settings select SSL for both incoming/outgoing.
Next screen you should see how often you want to set your gmail to update, so its you're own personal preference, but below that is a download messages box. It will let you select how far back your mail goes. I'm not sure how many messages you have in your inbox, but I use the All messages setting. Since I archive my messages constantly and put them to different folders, my inbox never gets more than 100 messages. You also shouldn't experience disappearing messages now.
POP3 is a really antiquated mail server set up, since Gmail provides IMAP service for free you should take advantage of it since its a far superior service.
Last thing is that make sure that IMAP service is enabled on your Gmail account, you can check that under options under one of the tabs.