It's not clear that your problem was the same as mine. Mine was that I have contacts in WL Mail that sync with Outlook.com (aka people.live.com) and, when I clicked on 'clean up contacts', it merged the duplicates at outlook.com, but they still appeared
as duplicates in wl mail.
In the end, I decided it wasn't worth wasting any more time, and I got rid of the duplicates manually, doing a few at a time.
If you have too many to contemplate doing it manually, and your contacts are not duplicated in one of WL Mail or Outlook.com, I would try the following (bear in mind that I haven't tried it, but it seems to me that it should work and, as you'll have a backup,
you will be safe):
-back up (export) the GOOD contact list (the one that doesn't have duplicates)
-delete all of the contacts in the BAD list (the one that has duplicates)
-close down both wl mail and outlook.com
-open wl mail and outlook.com
If the above doesn't work, I'd try:
-backup (export) the GOOD contact list (you'll already have this if you tried the above).
-delete all of the contacts that are in the BAD contact list
-delete all of the contacts that are in the GOOD list
-close down both wl mail and outlook.com.
-open up either wl mail or outlook.com (i.e. the one from which you exported the GOOD contacts)
-import the GOOD contacts from back up.
-open up the other application, and the contacts should have synched.
I hope this helps or, at least, gives you food for thought.