Hi Coolemail,
After we import the Outlook data file into an Office 365 account in Outlook, it will take times to sync the changes between Outlook and Office 365 based on the internet connectivity and the size of the data file.
Based on your description, after you import the file in Outlook, all the folders can be synced to Office 365 without issues, I suggest you import the data file in Outlook (configured as an Exchange account) with either the Exchange Cached mode or the Online mode, then wait for a while to see if the mail items can be synced to Office 365.