I think you're looking for <set/>. This is used to change existing values in XML.
For example, in my ReducedGlue modlet, I change the required amount of bones needed to make glue with the following:
Code:
<set xpath="/recipes/recipe[@name='resourceGlue'][@craft_area='campfire']/ingredient[@name='resourceBone']/@count">5</set>
<set xpath="/recipes/recipe[@name='resourceGlue'][@craft_area='chemistryStation']/ingredient[@name='resourceBone']/@count">3</set>