Price is set at simple product level in Magento 2 (and configurable products will inherit the special price from simple products beneath it).
The quickest way to do it correctly would be to use the REST API inside a script. This is the best way if you're a beginner - Magento has created this as an interface for external integration which should be used wherever possible.
http://devdocs.magento.com/swagger/index_20.html#!/catalogProductRepositoryV1
The correct endpoint is catalogProductRepository's PUT /V1/products/{sku} -
Note that you need to put the storeview code into the calling URL as described here.
http://devdocs.magento.com/guides/v2.0/rest/rest_endpoints.html
Here is a good post on using a script with the REST API
GET or SET Product special price using REST API
Another option is to import a multi store CSV using Magento 2 import functionality - this is best if you're not familiar with Magento/PHP development:
Here is an article about it:
https://www.alexcorradi.org/blog/a-guide-on-how-to-import-export-products-in-magento-2
Otherwise if you have a test environment and are more confident with coding you can create your own script to update:
Inside a class you'd have:
protected $action;
public function __construct(\Magento\Catalog\Model\Product\Action $productAction) {
$this->action = $productAction;
}
public function updatePrice($productIds, $data, $storeId) {
$this->action->updateAttributes($productIds, $data, $storeId);
}
then to run it use the following;
$specialPrice = null; // OR '' can't remember off the top of my head which clears it - perhaps either.
$data = ['special_price' => $specialPrice];
$storeId = 1; //whatever store id you like
$productIds = [1,2,3,4,5,6,7]; //whatever product ids you wish to change.
$this->updatePrice($productIds, $data, $storeId);
run for each store.
Apologies for any mistakes, I am just typing by memory. Please run on a test environment first!