The latest version of server edition is single-business. This is to allow features such as customer, supplier, employee portals which are already implemented in some limited way.
So if you launch server edition without command line parameters, you will be asked to import your business which is the file with .manager extension.
The only way to have multiple businesses in server edition would be to launch server edition multiple times on different ports (one for each business). I might create some sort of control panel which would make this easier to manage.
This maybe due to a conflict between the change in filenames structure.
Prior to version 17.4.0 the file names were a mix of alpha/numeric of about 15 characters.
After version 17.4.0 the file names became real names - the actual business name.
So your backup desktop version of 16.12.0 would have alpha/numeric file names and if your server version is after 17.4.0, then it is looking for real names.
You could update your desktop version to 17.5.n which will convert the filename structure, then attempt to import them into the server version.