You are attempting to import data to Exchange Online mailboxes using the PST Capture Tool 2.0 (http://www.microsoft.com/en-us/download/details.aspx?id=36789). The following works:
1. You can import PST files to the tool
2. You can map the PST files to mailboxes in Exchange Online (x64 bit version of Outlook is required to see the mailboxes)
3. If you open the PST file in Outlook on the machine, you can see all the content
When starting the Import, the stage called “Transferring” completes 100%. Then, when the Import stage begins, you can see that it only finds 2 folders. The progress shows Importing Folder 0/2, 1/2 and then 2/2.
After the import is done, you can see in the Exchange Online mailbox that the only content that have been imported is the Deleted Items folder.
This occurs if the PST file that is imported is in an incompatible format. Without going into, or knowing, the details of it all, PST files can be created in different structures. The version of Outlook together with how PST Capture Tool 2.0 works decide if all content in the PST files root folder (IPM_SUBTREE) will be visible to the operation or not. Read more here: http://msdn.microsoft.com/en-us/library/ff387699(v=office.12).aspx
The error can occur when the PST file have been exported from Exchange Server 2010 SP3 using New-MailboxExportRequest.
Run SCANPST.EXE from the Program Files\Microsoft Office\(VersionNumber) folder on the machine. Use SCANPST.EXE to scan and repair the PST files you want to import. After repairing the file, PST Capture 2.0 will import all folders and objects.
This process takes a while, and if you are to do 100+ mailboxes, it might have a severe impact to your planning. Depending on the PST file, it might help to change Outlook version on the machine where you run PST Capture 2.0 – just make sure that it is always x64 bit.