Ummm, have Siteworx fix their bug?
You generally wouldn't be "placing" files in these directories. They would be uploaded via the application and referenced by the application.
You could run the following SQL(assuming your MAX_FILES_IN_DIR value in config.local.php is 1000).
ALTER TABLE cs_cart_images AUTO_INCREMENT = 1001;
This will cause the next image_id to be 1001 which would then cause new images to start in the '1' directory rather than the '0' directory.
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