Unfortunately, it's an issue we're aware of and we're going to address in the next update of our Outlook plugin. Right now, moving emails (especially when using an Exchange Server) may indeed change or influence their unique IDs.
Please note that you can forward emails to your Todoist project directly instead of linking them. We've explained the advantages of this option on our blog: http://todoist.com/blog/2013/01/zero-inbox-policy-with-todoist/
Thank you for the reply, I would wait for an update for the Outlook plug-in.