It is possible but very tedious process.
Basically you would need to design a script that would import/export all records in your database. So that when you upload the "newly updated" database on FMS, you can run this script to update the records on the "newly updated" database with records from the old one. And this only works if you don't add new fields or modify any relationships. Making new or modifying layouts and adding or modifying new scripts should be fine as long as you don't include newly created fields or layouts that uses a new relationship.
Again, it's possible but very tedious process.
Good news is, you can work on the hosted file directly. That's how FileMaker is designed anyway.
Put it this way, if you're scared of breaking something important if you work on the hosted file directly, don't even think of doing anything that I just mentioned above.
Believe me, you're not the only person that's surprised.
I know what you mean. But it's perfectly safe to work on the database that is hosted.
Of course, you need to make backups just in case.
It may be safe to work on a hosted database "live" but it's important to be absolutely certain no clients are logged in. Otherwise data loss is possible. And of course, as mentioned above, having at least one backup is essential. It's easy to disconnect all clients using the Admin Console, but that doesn't prevent a client from logging in again. A more secure way is to close all databases, download them, make changes then upload the revised databases via FMP client.