The system isn't set up to delete from the Inbox.
Have you recently set up any new email collection app or mail collection service? If anyone has set up a POP3 account with default settings for your email address and password then that can download and delete mail messages from the Inbox.
As a precaution you should upgrade your email password to lock out any unauthorised device or service from connecting to your mailbox.
If you need further advice then just let us know.
