DEVONthink does not automatically protect you from data loss – that is your responsibility.
Whether you use File > Export > Database Archive…, or backup your computer and DEVONthink data using some other method, you should backup your databases at least daily.
If you have indexed folders and/or files into your database, make sure your backups include those external folders and files.
When you archive a database you should have a zip file such as:
MyDatabase.dtBase2.zip
When you unzip that, you should have
MyDatabase.dtBase2
This is the database. It is a “package”, a type of macOS folder whose contents are not normally visible. What you describe is what happens when you either (a) remove the “.dtBase2” extension and cause the folder contents to be exposed, or (b) choose “Show Package Contents” from the contextual menu and cause the folder contents to be exposed.
In either case, do not muck around inside the .dtBase2 package.
If you want to restore an archive, close the database that was archived and move it to a secure location. Open the database that was just unzipped.
Do not open both databases at the same time – because of unique identifiers for the database and its contents, you should only have one instance of a database in use at any given time.
You shouldn’t see “unzipped files”. You should see either a .dtBase2 file or a folder with the database’s name. If it’s the folder, add .dtBase2 to the end of the folder name.