I've never used the annotation feature in the Kobo but I thought that your annotations, bookmarks etc were all saved when you synced? Supposedly notes you make on your Touch should be available on the Kobo app on your iPhone or on your Desktop app or (in your case) another Touch which syncs to the same account.
If you ask on the Kobo forum I'm sure someone who uses that feature could help you.
BTW what incredible bad luck to have 2 ereaders fail!
