You should be able to receive the war loot even if the Command Post is under upgrade.
If you didn't receive it, you might want to reach out to Customer Service, and they might be able to help you with a compensation, if you haven't received it due to a bug. Earlier, there used to be a set of questions which CS used to send, asking for responses when you submit such a complaint. Upon answering them and sending your response, typically, they used to compensate with some crowns (probably after some due diligence and verification from their side).
Hope this helps!
Cheers, and happy gaming!