To delete all bookmarks in a PDF document, simply create a new empty root bookmark.

With jPDFProcess, use PDFDocument.createRootBookmark();
With jPDFAssemble, use PDFAssemble.createRootBookmark();
With jPDFEditor, use PDFEditorBean.getDocument().createRootBookmark();

Here is sample code to do so:

// Load the document
PDFDocument pdfDoc = new PDFDocument ("input.pdf", null);
// Get the root bookmark, create one if necessary
Bookmark rootBK = pdfDoc.getRootBookmark();
// if there is a rootbookmark, make sure it's empty
if (rootBK != null)
   rootBK = pdfDoc.createRootBookmark ();

With jPDFNotes, it is possible to delete the bookmarks by removing all children in the root bookmark:

int count = 0;		
// We can leave "outlines" entry in root dictionary, but should remove all bookmarks
Bookmark root = mPDFDocument.getRootBookmark();
if (root != null)
 int childCount = root.getChildCount();
 for (int i = 0; i < childCount; i++)
    // remove these in reverse order since it could alter the array
       root.removeChildBookmark(childCount - 1 - i);
    catch (PDFException e)