As long as you understand how the pins file is utilized (and do make a backup or keep a copy of the original) there aren't any real concerns about fiddling with it.
Worst-case scenario, you can always reinstall the IDE if things got totally messed up. But just keeping a backup copy of that one file should be all you need.
I've done what you're discussing with Sparkfun's pro micro (a Leonardo clone), created my own pins_arduino.h for it that suited my requirements.
The only other caveat is if you are using any libraries, just make sure you update any hardcoded references they have, eg. the SD card library has d4 hardwired as the chip select pin, so if you've redefined d4 then you might need to modify the library.
Cheers!