Hi!!
Thank you for the comments!
I understand that if the file is completely loose I can reinstall the arduino IDE, this is the easy part. 
My concern is about changing a pin that could be related with a Timer a port or something like that and this new mapped pin could interfere with the actual arduino core code.
Actually I think my question is: If I remap the pins in the pins_arduino.h file will I need to chance other piece of the arduino code?
I know that the RX and TX leds are defined and used on the bootloader (Caterina.c and .h - Leonardo) and also inside the USBCore.cpp so I need to change them. But how to know other parts of the arduino code are related?
Good point about the 3rd party libraries, I'll keep an eye on that.
Thank you.