QDoc: Problems with (QML) modules and .index/.qhp files

We changed the URL we want for modules and QML modules and this does not get refelected in the .index and .qhp files.
For example the qtcore module page is now qtcore-module.html, but in the qhp file still qtcore.html gets inserted. To me it seems that the FullDocumentLocation could be the problem, even though that should be correct, because we set the correct URL in the fileBase (and it works if you build everything in one go, just not in the indices).