Usually you can simply copy and paste your keybindings and templates (or any other setting) from your old Game.prefs - Just poke around and make a backup, then you can test it. In the worst case, you can simply restore the backup and try again.

@indexlibrorum It is the primary in windows. I have FAF running in single monitor, windowed mode with the window spanning both monitors and running dual screen inside FAF (not dual monitor). FAF doesn't have a setting to designate right/left as primary.