Hi WarrickW,
Generally, if we successful import PST file into Outlook client, emails will be synced to Exchange Online. Since I notice you have set retention policy to archive email older than 2 years, could you enable archive feature for user and check if emails exist in the user’s archive folder? Also, you can check if it can be recovered via Recover Deleted Items at OWA or Outlook client. Moreover, the size of emails is too large and it may take several hours to sync complete. However, you can create a new mailbox for testing.
Here are some useful articles for your reference:
Recover Deleted Items
Recover Deleted E-Mail Messages in Exchange Online
Thanks,
Johnny Zhang