Where does filezilla server store its users data?

Try looking at FileZilla Server.xml in your install directory.

In current FileZilla-Versions look into %USERPROFILE%\AppData\Roaming\FileZilla. The sitemanager.xml inside this folder contains the wanted information. For migration, it is possbible to copy the whole FileZilla-Folder from one Windows installation to another (or one Windows user to another).