That's not exactly true, Rog. If two people have changed the file, which causes a conflict, then you have resolve the conflict manually. Recreating the file with godeps would populate it with whatever commit happens to be in your gopath right now, which has no relevance to what is conflicted in the file and could be a completely different hash.
I tend to check out one branch, run godeps -u, then check out the other one and run godeps -N -u. Then you've got the newest deps from both branches. I still wouldn't resolve the conflict manually.
Aside: the conflicts mentioned in the article should never be a real problem because you can always resolve the conflict by just recreating the dependences.tsv file (you should never be editing it manually anyway).