Yes, Stack is the binary closed source code.
In Upgradable Stack OTA, there is two options - either for upgrading your application only, or to update the stack as well.
The upgrading of stack means, upgrading the entire BLE library files from previous BLE stack to the next BLE stack .
The GATT server modifications like writing a new value, changing UUID all will comes under application level upgrade.
For additional info regarding firmware upgrades in Cypress BLE, you can refer our appnote from the link: http://www.cypress.com/documentation/application-notes/an97060-psoc-4-ble-and-proc-ble-over-air-ota-device-firmware-upgrade