If I remember correctly from when a mate and I attacked his, the rivets that look 2 peice units need a small screwdriver to flip the top part open, the whole thing can then be pulled out with pliers, the other clips which just look like one solid head they got drilled out and replaced as they are plastic rivets, we just had a bag full of various plugs and used the best fit, think we just pushed a plug in when we put everything back .... Supercheap is your friend........
UPDATE: a quick phone call and yes the solid looking head jobs are plastic rivets but neither of us are sure what we replaced them with....... I wouldn't want to use a normal rivet for corrosion issues..... and the flares fit into clips which we think came out sideways..
On my HilUx I got caught the same but just drilled a neat hole in the guard liner and zip tied it all back, temporary of course works well (temp being about 8 years so far).
pic of genuine rivet,