From SQF Code:
The scope of certification specifies:
The site. SQF certification is site specific. The entire site, including all premises, support buildings, silos, tanks, loading and unloading bays, and external grounds are identified and included in the scope of certification.
If activities are carried out in different premises but are overseen by the same senior, operational, and technical management and are covered by the one SQF System, the site can be expanded to include those premises.
Glossary definitions:
Site: The specific location where an SQF Food Safety or Quality System is implemented by a food business involved in the production, manufacture, processing, transport, storage, distribution, or sale of food, beverages, packaging, animal feed, or pet food.
Site Audit: The on-site component of a certification or re-certification audit that reviews the site’s products and processes to determine the effective documentation and implementation of the site’s SQF Food Safety or Quality System (refer to “on-site visit”).
By not including the separate warehouse where you're conducting storage and transportation activities, you've misrepresented your site to the SQF auditor and certifying body.
In appendix 3 of the SQF Code:
2 Conditions for Use
2.3 Subsidiary companies and site addresses not included on the certificate of registration are not certified to use the SQF logo.
Your product stored under the unlisted site is not covered by your SQF certification and cannot be implied as such to your customers.