I need to clarify before anything else here, we do not disable or switch off your site when your key shows as invalid. Not in any way at all. We would also not change any settings in any way for any other reason, unless you are running an upgrade and it tells you as much.
Given the above, there is something that has happened on your server to cause this, which you will need to trace down. From what you have said, this sounds very much like someone has been messing in your admin CP, or on your database. So I would track those first of all.
The license key issue is likely due to not being able to contact the license server at the time. That would simply need a refresh, and would only remove that message, and enable you to do things such as access marketplace, and run the spam service and run upgrades. Nothing else in any way is affected by this.
Have you managed to recover from the issue, or is there anything else you need assistance with to correct?