If you are using a POP3 account and you are deleting them from your phone, they will show up as deleted on your PC. If you delete them from your PC they will disappear from your phone. With that being said, go to your inbox > tools > options there are some settings you can try.
- download messages from - Today, last 3 days, last week, 30 days....ect.
- move deleted items to - trash or server trash - if you move to server trash you will be able to see the deleted item in your trash if you login to your POP3 account on your PC
Good Luck