If the default repository list was changed in Nailgun, 'fuel-package-updates' changes link for only the first (upstream) Ubuntu repository. All additional upstream and mos repositories are left unchanged (see attached screenshot).
Example:
[root@nailgun]# fuel-package-updates -d ubuntu-baseos -r 2014.2.2-6.1 --no-download --make-default --apply -s 10.109.30.2 -p admin -b http://10.109.30.2:8080/ubuntu-part -e 2 --clear-upstream-repos
2015-05-22 15:18:22,361 - INFO - Skipping repository download...
2015-05-22 15:18:22,363 - INFO - Updating environment repositories...
2015-05-22 15:18:22,363 - INFO - Updating default repositories...
2015-05-22 15:18:22,369 - WARNING - Authorization failure: Authentication required
[root@nailgun]#
Result is on the screenshot.
So in looking into how this could be accomplished, I don't think it's correct to remove customized ubuntu repos. It currently works correctly if you do not add additional repositories for the ubuntu repos. Did the ubuntu-{0,1,2,3} repos get added via a native fuel process meaning we should handle for the name matches for ubuntu-{0,1,2,3}?