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I'm using a 3rd party plugin to setup our production website in a test/dev environment. It allows export/import of the categories, excluding the Category ID's (which are automatically generated).
As a test, we created a full list of categories and a single product. Exported both, wiped both the product and categories, and the import works. Except that the Category ID's are being added incrementally (instead of being "reset" when I delete the categories). This makes sense from a Db perspective, so I'm assuming that the Category ID # is being incrementally counted from some Db count location.

Does anybody know where this count is coming from, and where I can reset it in Magento 2.1 ? (this is just for testing purposes).

Thanks in advance.

If you delete categories from admin panel, newly created categories will be having an id based on last created category id(irrespective of whether it's present or deleted). You need to truncate these categories using following sql queries which will reset the ids. Take db backup before executing it.

 SET FOREIGN_KEY_CHECKS = 0;

 TRUNCATE TABLE `catalog_category_entity`; 
 TRUNCATE TABLE `catalog_category_entity_datetime`; 
 TRUNCATE TABLE `catalog_category_entity_decimal`; 
 TRUNCATE TABLE `catalog_category_entity_int`; 
 TRUNCATE TABLE `catalog_category_entity_text`; 
 TRUNCATE TABLE `catalog_category_entity_varchar`; 
 TRUNCATE TABLE `catalog_category_product`; 
 TRUNCATE TABLE `catalog_category_product_index`;

 INSERT INTO `catalog_category_entity` (`entity_id`, `attribute_set_id`, `parent_id`, `created_at`, `updated_at`, `path`, `position`, `level`, `children_count`) VALUES ('1', '0', '0', '2016-06-23 00:00:00', '2016-06-23 00:00:00', '1', '0', '0', '1'), ('2', '3', '1', '2016-06-23 00:00:00', '2016-06-23 00:00:00', '1/2', '1', '1', '0');
 INSERT INTO `catalog_category_entity_datetime` (`value_id`, `attribute_id`, `store_id`, `entity_id`, `value`) VALUES ('1', '58', '0', '1', NULL), (2, 58, 0, 2, NULL);
 INSERT INTO `catalog_category_entity_decimal` (`value_id`, `attribute_id`, `store_id`, `entity_id`, `value`) VALUES
 (1, 69, 0, 2, NULL);
 INSERT INTO `catalog_category_entity_int` (`value_id`, `attribute_id`, `store_id`, `entity_id`, `value`) VALUES ('1', '66', '0', '1', '1'), (2, 43, 0, 2, 1), (3, 50, 0, 2, NULL), (4, 51, 0, 2, 1), (5, 66, 0, 2, 1), (6, 68, 0, 2, 0);
 INSERT INTO `catalog_category_entity_text` (`value_id`, `attribute_id`, `store_id`, `entity_id`, `value`) VALUES ('1', '64', '0', '1', NULL), (2, 64, 0, 2, NULL), (3, 44, 0, 2, NULL), (4, 47, 0, 2, NULL), (5, 48, 0, 2, NULL), (6, 61, 0, 2, NULL);
 INSERT INTO `catalog_category_entity_varchar` (`value_id`, `attribute_id`, `store_id`, `entity_id`, `value`) VALUES ('1', '42', '0', '1', 'Root Catalog');
 INSERT INTO `catalog_category_entity_varchar` (`value_id`, `attribute_id`, `store_id`, `entity_id`, `value`) VALUES (2, 42, 0, 2, 'Default Category'), (3, 46, 0, 2, NULL), (4, 49, 0, 2, 'PRODUCTS'), (5, 57, 0, 2, NULL), (6, 60, 0, 2, NULL), (7, 65, 0, 2, NULL), (8, 113, 0, 2, 'default-category'), (9, 114, 0, 2, NULL), (10, 143, 0, 2, NULL), (11, 145, 0, 2, NULL), (12, 147, 0, 2, NULL);

 SET FOREIGN_KEY_CHECKS = 1;

If you have phpMyAdmin then you can do by going to table and clicking on Operations. After that you see a AUTO_INCREMENT which in my case is 42. You can reset it to 1 and it should solve your problem.

If you have command line access only then you can run the below mysql query:

ALTER TABLE `catalog_category_entity` AUTO_INCREMENT=1