When I delete Yahoo email messages on my phone they still remain on the main account, even after syncing. It works the other way around. I cannot find a setting to fix this.
I'm having the same issue on my Samsung Stratosphere, but only with the most recent app update. I thought I had figured out how to get around it - by deleting the emails on my phone then emptying the trash folder, but when I checked email on my desk computer, not only were the emails still in the inbox, but the trash was still full. Grrrrr....