First of all, the .fwb file is portable and can be copied back and forth between Linux/BSD and windows machines. Even comments and object names entered in a local language should be preserved since the GUI uses UTF-8 internally.
Built-in installer relies on path settings for ssh and SCP in. Since preferences are stored outside of the .fwb file, the installer should work just fine when .fwb file is copied from Unix to Windows and back. Just configure the path to ssh program in preferences on each system using default settings "ssh" on Linux and path to plink.exe on Windows and give it a try.
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