Microsoft has been notified that in some situations, users are noticing that either whole emails are missing or the body of the messages are empty.
We've noticed that this is also effecting our users as when an email is moved either to the Inbox or Sane folders, the message appears to disappear.
They have concluded that main cause of this is because Conversation View is being used.
To work around this issue, turn off the Conversations View.
If you are still noticing issues, make sure that your Arrange by is set to "Date" and the View is set to "All" as seen in the image below: