When using the dialog to configure KMail and specific the Local Folders, using Change to edit the configuration of Local Folders, the text field with the name of the maildir folder shows /home/freek/.local/share/akonadi_maildir_resource_0 . This maildir folder contains a number of messages in subfolders .../*/cur . However these massages are not displayed in KMail. KMail shows other messages in trash. Searching in ~/.local/share/ I found a folder 
~/.local/share/.akonadi_maildir_resource_0.directory which contains these messages in a subfolder trash/new/ .

Prevously, yesterday, I had another Local Folders where the maildir folder was 
/home/freek/.local/share/0/akonadi_maildir_resource_0; I deleted that entry in the configuration dialog of KMail.
However in ~/.config/kmail2rc there was still an entry: 
[Resource akonadi_maildir_resource_1], which should have been deleted by the above action.

Searching in ~/.config for configuration files for KMail I did not find any reference to this ~/.local/share/.akonadi_maildir_resource_0.directory .
File .config/akonadi_maildir_resource_0rc did contain the reference to
$HOME/.local/share/akonadi_maildir_resource_0


Quite confusing, consider it a bug.