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)