We have implemented our own custom activity for deletion of multiple highlights/notes. But once we delete these from the activity the pdf doesn't reflect the changes immediately. Currently for the changes to take effect we have to re-open the book.
The PDFViewCtrl class has an update(boolean) function that can be used to redraw everything, without having to close the document.
If you are using CompleteReaderPDFViewCtrl class, then this class extends PDFViewCtrl, so same applies.
For example see TabbedVierwerFragment.java file and search for mPdfViewCtrl.update(true);