This can happen because it is impossible to deactivate an item in the marketplace, because this process is not part of the integration. In other words, deactivation can only be done in VTEX.

For an SKU to be inactive with a partner, this has to be configured in the marketplace, and you must contact them direct.

If a purchase has been made, you can accept it, activating the item for the order to be integrated, or refuse integration.