(including removing the old chapters/instal./.xml)?
There's no hurry to remove the old files;-)
The hurry is just because 'make test' will fail if you don't delete those files (because of ID colisions)
Ehem, you don't need to remove files, you just need to remove the references to them. But only later when the new install stuff is ok for publication, and not in an intermediate state.
Goba