You would have to use IMAP instead of POP3 on all your accounts to achieve this.
This way the master copy of emails you have is dictated by what's on the server. The devices that connect to the server (PC, phone, webmail, etc) will see just the emails that are on the server. So in other words, all devices see the same email list.
If you delete an email on your PC, it will update the server. When the phone connects it will refresh its list of emails and hence the email you deleted on your PC will disappear from your phone too. And vice versa.
Just remember though not to delete any emails you haven't read or want to keep. If you delete it anywhere it will delete everywhere with IMAP.

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