I use Thunderbird. I think it is the best email client for Linux. However, I noticed that it doesn't delete messages. I googled it, found out it is a common problem, many are faced with.

Someone suggested, it hapens when you have multiple acounts.

I got the solution from someone clled Toad-Hall on Mozilla forums.

Here is the solution:

1- Close Thunderbird
2- go to your file manager (Dolphin, caja, Nautilus, sunflower,......) what ever you are using
3- go to View and choose, show hidden files
4- Locat folder caled .Thunderbird
5- inside that you will find a folder looking like 7orl2sk0.defualt, open it
6- then open Mail folder
7- here you will see folder pertaining to all the accounts you have.
8- open them one at a time and delete: folder Trash, and file Trash.msf
9- Now open Thunderbird. and you will be able to delete email