Mac collected from customer support, some settings have been reset Yesterday I collected my Macbook Pro from an authorized Apple Service Center, where they replaced some hardware components (logic board and battery-trackpad-keyboard block).

The SSD drive has not been replaced (according to the invoice), and it was encrypted with File Vault (OS X 10.9.3).

And yet, some settings have been changed. The ones I am 100% certain about are:  


Accessibility settings, ignore built-in trackpad when a mouse is present.
This was definitely checked, but it has been disabled.
other trackpad settings: tap to click. This was enabled and it's now disabled.


Is it because the trackpad has been replaced?
I also did enable filevault right before bringing my mac to the service center, and I didn't really have time to notice any change then. Can these changes depend on file vault?
Some settings in OS X are “per machine” which is mostly derermined by MAC address. Since you for a replacement logic board that address has changed so OS X is using defaults since the settings for the former logic board do not match the hardware it is currently running on.
This is normal and expected. Just set them again to your liking and you'll be fine.