Actually managed to fix this using a different method to @Jared Kipe's method although continued to comment on his approach as no doubt it would have been a safer and more practical solution than mine.
Within the MySQL database, I removed all records from the following tables relating to the store_id in question:-
catalog_product_entity_datetime
catalog_product_entity_decimal
catalog_product_entity_gallery
catalog_product_entity_group_price
catalog_product_entity_int
catalog_product_entity_media_gallery
catalog_product_entity_media_gallery_value
catalog_product_entity_text
catalog_product_entity_tier_price
catalog_product_entity_varchar
When dealing with thousands of records like I was, this is far quicker executing the queries to handle this, for example:-
DELETE FROM `db_name`.`catalog_product_entity_*` WHERE `store_id` = 2;
(Where you replace db_name with the name of your database and the * with each of the appended names to the table.
This then ensures that for the store_id '2', all product configuration is reset back to 'Use Default Config'.
I'm keen to receive other answers and test out in order to ensure that the best approach to my original issue is highlighted here for future use. I actually think I encountered a bug in Magento as I can't see how the import process could have possible wiped all product data for multistores based on minimal (if at all) change in the CSV that it exported out. Lesson to be learn that writing a script as @Jared Kipe suggests will likely prove the best method, and maybe import dataflows (which I've just created a custom one to update all wholesale pricing and it has worked flawlessly by the way).