the whole store; the entire shop
Refers to a single store in its entirety, often used in contexts like sales or events covering the whole premises.
全店でセールを実施します。
We're holding a sale throughout the whole store.
all stores; every shop
Refers to every store in a chain or group, commonly used in retail announcements.
この商品は全店で取り扱っています。
This product is available at all stores.