There's nothing in wp-admin that will help find where the template is used, but you could try querying the database. If the template is assigned to any posts, you will find that template ID in the postmeta table under they key '_views_template'. That's where I would start. It may be assigned to posts in the trash, or somewhere else that isn't obvious. Let me know if this doesn't help track down the template assignments.
Are you sure its the post meta table I have to query?
Yes but it seems I was not clear enough with my explanation. Instead of querying this table by meta_key = _views_template and post_id = 1065, try querying for meta_key=_views_template and meta_value = 1065. A meta_value of 1065 indicates the Content Template with ID 1065 is assigned to a post with ID = [post_id]. Once you identify those posts by ID, you can edit each one individually in wp-admin to unassign the Content Template 1065, or assign a different one.
But is it really possible that you can delete a custom post type in Types, without deleting the posts with that type? It may be a bug that has been fixed, since I deleted the post type?
Actually the Types software is not designed to delete all the posts when you delete a custom post type. The posts will remain in the database unless you delete each post individually. I suggest deleting the individual posts before deleting the post type if you'd like to remove the individual posts from the database. If you have already deleted the custom post type in Toolset > Post Types, you could recreate the post type temporarily using the same slug. Then you would be able to delete the individual posts from wp-admin. After deleting the posts, you could again delete the post type again in Toolset > Post Types.
I still think its a mistake not at least to tell the user that there will be remaining posts in the database. I know its a common plugin way of thinking that you delete the plugin but not the settings.
I think this is the wrong way to treat the deletion, and the user should get the option of keeping the data or deleting it.
Our second tier team has created a feature request to allow Users the opportunity to delete all posts in a custom post type when deleting the post type. I'll let you know by updating the ticket here if our developers are able to include this feature in an upcoming release in the near future. Thanks for your input!