The FTP and MySQL credentials are removed from the cloud vault and from your PC, together with the project's settings on every PC signed in to your account; every manager loses the project and is notified by email (the owner too, when a manager removes it), and pending invitations stop working.
Your website is not touched: its files and its databases stay exactly as they are. The only file SyncNow removes from the hosting is its own database gateway, if it installed one, and your local folder and the activity history are kept.
The owner or a manager removes a project with Remove project in the ... menu of its row or the red Remove project button in Project settings, after a confirmation that lists what is removed and what is kept. It cannot be undone: to work on the project again, the owner adds it back and enters its credentials. A manager who only wants to stop working on it leaves instead, see How do I leave a project I was invited to?.