[Dovecot] Index issue?

I've just hastily migrated from Dovecot 1.2.9 to 2.2.9 due to a disk crash.

When I say hastily, I literally copied the user's mail data files to the new server and then started the Dovecot service.

The trouble is, I now have a user who can see all the subfolders of her inbox in Outlook, but not on her iPad.

Do I need to re-index her mail folders? The data is there (as seen by Outlook 2013) and is good, but the iPad mail client only sees the top-level folder.

Any thoughts?

-Mark