Is there a way inside or outside of uVision2 to fill my output intel hex file so that unused bytes are set to 0x00? So that when I actually program my chip I am sure that every byte is programmed.
Usually this option exist in chip-programmer software. Also, you can convert *.HEX to *.BIN using HEX2BIN utility with option /Pn - pad data, n=0. Then load *.BIN as binary data. If you still need *.HEX format you can convert resulting *.BIN to *.HEX using BIN2HEX utility.