If you have multiple projects with Tycho and separate targetdefinitions for these, Eclipse and the headless buildsystem will give errors, that the features from your automatically published updatesites are not found. For now, I found the possibility to set the version manually in the targetdefinition to ‘0.0.0’, so the system won’t complain. The newest version is taken.
If you are only using your Nexus or local repositories, you can use the flag
-Declipse.p2.mirrors=false for an eclipse instance, to forcefully disable all mentioned mirror repositories.