So, if another nation or body of nations have the hypothetical ability to decide at some point they don't like an entity being sovereign, that entity is not? Looks like you just proved that no nation is sovereign, because neighbor states or even the UN might at some point formally declare "nah, we don't recognize X as a sovereign nation anymore", done.
An entity ceases to be sovereign when it loses either independence or authority over its territory, or when it ceases to exist altogether.
Nations can willingly submit to international treaties, but they can also unilaterally ignore or exit them. They can do whatever they want at home. Another, more powerful nation can decide that it deserves invading them or toppling their government by force. When a government changes it policies because of the (perceived) certainty of an invasion if they don't, you can put their independence in question, and thus their sovereignty. Yes, a few years ago, the idea of an "international community" bound by UN decisions did exactly that for a lot of countries. Just like in Shadowrun, the threat of Corporate Court economical sanctions appears to be enough for most countries to no longer be truly independent and sovereign.
Megacorporations on the other hand, adhere to the Corporate Court charter, which contains, along with the Business Recognition Accords signed by most countries, provisions which
require all these corporations and countries to stop accepting a corporation's authority over its properties when the Corporate Court says it no longer fulfills the requirements.
A corporation cannot seriously expects its security and military forces would be able to hold off all the other megacorporations and all the countries it operates in from exerting their authority inside its facilities, while dealing with the economical sanctions. Only the Big Ten may possibly consider that they are so important for the world economy and have enough WMD at hand to ensure economical or military MAD (like the US or China nowadays) that it puts them in a gray area were they're neither truly independent nor really dependent, but
interdependent.