Hi Roy,
From your post, I'd like to confirm the following things:
1. The online inbox is empty. Could you find the emails in other folders, such as Deleted item?
2. Please check whether other folders are also empty, such as Calendar.
3. Do you set up other clients to access Office 365 account, such as mobile device or Outlook desktop application?
Under this situation, I suggest you try the following steps:
1. Log into Office 365 OWA.
2. Check if the emails are in Deleted Items.
3. If the emails are not in Deleted Items, please right click Deleted Items and select Recover Deleted Items.
4. Check if the emails are in Recover Deleted Items.
Thanks,
Edward Qu