We have been experimenting with syncing our existing database(not Magento) to Magento 2.0.
In the process we have created over 1000 categories, but then we rearranged all the IDs to sync with our system. The problem is that I can no longer import the new categories as I get the error "URL key for specified store already exists." and we are getting duplicate categories now.
I think the best solution would be to clear them all out and import fresh. I found this tutorial for 1.9