Be careful in which order you clean things. With the old setup it didn't matter. If you want to remove a package don't do
rm -r Hat/Pack cd $DAVINCIROOT/cmt ; cmt br make clean
This will not remove the package library from the InstallArea. Only the package knows how to clean its libraries. So do:
cd $DAVINCIROOT/cmt ; cmt br make clean cd ../../../../ ; rm -r Hat/Pack
Here the first step will have cleaned the InstallArea.
Of course this does not only apply for DaVinci but for all cmt packages. (Instructions copied from https://twiki.cern.ch/twiki/bin/view/LHCb/InstallAreaWiki)