I have to create a number of new stores inside my Magento installation. One thing that this does is forces me to have to do a LOT of reindexing on the entire site. For most
The best way I've found to get around this is make sure you you have no pending indexing processes, if so take care of them BEFORE this as well as making a database backup:
Admin -> Catalog -> URL Rewrite Manager.
Request Path search for "-1.html" (minus double quotes)
Remove all of them and re-index "Catalog URL Rewrites" Under System -> Index Management.
I believe the duplicates come about from stale or improper indexing when creating a new product its inserted, then during indexing a duplicate is created.
Hope this helps.