When the company no longer exists the only way to get the territory back is for someone else to declare war and take it. You cannot do upgrades on it and the taxes that territory produces just, well, vanish.
There is nothing you can do but hope another company declares war, then your company can declare war back and take it back.
We are currently experiencing this on my server. A company has completely disbanded/transferred and now the territory cannot be declared on. We have had multiple company leaders attempt to declare war on the territory but nothing happens. (we are not attempting this while an invasion is active or anything, it allows us to go through the process of selecting the type of war being declared, but when you click continue, nothing happens).
The company that left, left without replacing the leadership of their company and now that territory is basically useless. We have checked on the guild page, and sorted by territories claimed, and our server is stating that there are only 10 claims to land on our server, even though there are 11 territories and all of them are currently being controlled by a faction.
How does this even happen? You can’t transfer server without leaving company and you can’t leave the company as Gov without giving Gov to somebody else, right?