We've learned that SM doesn't work well with Outlook Desktop if folders exist within the Inbox. The recommendation is they should exist outside the Inbox. 99% of our users have all of their additional folders in the Inbox because Exchange/Outlook were OK with that but we have sync issues particularly with larger accounts. The users don't seem to care at all if the folders are moved because they lose all their message rules in Outlook Desktop when the account is replaced anyway. 

Idea: offer to move the folders outside of the Inbox during migration. That would avoid me having to impersonate every user and do the moves myself. That is going to take a long time.