My boss told me to alter the business proposal so that it emphasized the mutual benefits more.
You change again. This is more along the lines of an alteration, because you changed once in order to get to where you are, and then you get changed again to become altered, which is why it's an alteration (though change works too).
This is a jukugo word, which usually means on'yomi readings from the kanji. If you know the readings of your kanji you'll know how to read this as well.