If you want users to be able to retrieve their archived items via shortcuts, then you need to keep the EV hidden message in their mailboxes. You say this:
"As users have shortcuts in their outlook profiles, so post moving the mailboxes to office 365 the hidden message from the mailbox will be moved / deleted."
But I don't see any reason why this must be true. The EV archiving task will not be able to place new or updated hidden messages into the O365 mailbox, but if the user already has a hidden message, the EV Outlook Add-in will continue to read it and allow shortcut retrieval. I worked with a customer quite recently who was doing this very thing, coasting off of existing hidden messages so that the EV Outlook Add-in could continue to retrieve shortcuts and provide the Search Vaults button, even though the mailbox lived in O365. It works.
So just don't delete the EV hidden message when you migrate the mailboxes and you should be fine.
Also, before you migrate the mailbox, make sure you really like your Desktop Policy. Since you can't write a new hidden message, you'll be stuck with the one that's there when you migrate.
(Technically it is possible to modify the hidden message after you migrate, but it's an ugly and manual process that you'd prefer to avoid if you can.)
--Chris
