Heres what I did. I went to the local Pat Catans (art supply store) and picked up and exacto set similiar to
this one. Then I went to walmart and bought a set of sharpies like
these but I didn't get the ultra-fine point though I imagine they would work. I then used the square exacto blade to cut off the dimple on all the chips and used the corresponding sharpie to color in the white mark it left. After the labels are applied you can't hardly tell. Just test the colore first to make sure their a match.
Edit: Here's a link to the original thread I posted pics in. Halfway down you can see a scan of them. The yellow got distorted in the scan and you can see where I removed the dimple.
Pics. Also I answered a couple questions about labeling and such to.