I used this plugin to bulk convert my post types when I upgraded more fields and added more types. After trial and error, restoring my database, I was able to retain all of the custom taxonomies (and it was a lot) associated with each post. This was fantastic, however...
In the backend and in the database all seems in order but when I try to query by a taxonomy (e.g. 'city' => 'boston') the query returns no results.
It is really strange because I know the taxonomies are associated to the posts and I can call them in the theme but something is going very wrong when querying.
This is the last step to me completing an upgrade to 3.0.1 from 2.9.2 so if any one has any insight, please, all is welcome.