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Note that even if your BIOS supports swapping Fn and Ctrl, you may need a BIOS update to get proper functioning of certain ctrl key combinations. Per http://earthwithsun.com/questions/814975/lenovo-laptop-fn-ctrl-swap:
I have set up Ubuntu 14.04 on a new Lenovo E540 and choose the BIOS option
to swap the Fn and Ctrl keys. This works well but there are some quirks.
It appears Lenovo has introduced some extra keyboard shortcuts at BIOS
level in v2.13, such as Fn+S, Fn+B and Fn+P. Now with the Ctrl and Fn
buttons switched in BIOS, the shortcuts are still triggered when pressing
the physical Fn key (Ctrl key in software). This means pressing Ctrl+S is
intercepted and interpreted as Fn+S by the BIOS, and my code isn't saved.
BIOS version 2.16 (10/30/2014) fixed this issue finally :)
I just encountered this myself and spent about 4 hours trying to figure out how to fix Ctrl-S to work properly after swapping Ctrl and Fn, not being willing to go back to accepting the (very) unfortunate placement of the control key on Thinkpads. Thankfully, I found the earthwithsun entry and realized that I needed a BIOS update.