A digital ink annotation process and system for processing digital documents and digital ink annotations therein. The process and system maintain an annotation's position within a document such that the original intent and meaning of the annotation is preserved. This is true even if the document is edited, resized, displayed on a different device or otherwise modified. The digital ink annotation process includes automatic and manual grouping of digital ink strokes within a document to define digital ink annotations, classifying the annotations according to annotation type, and anchoring the annotations to appropriate regions or positions in a document. The process further includes reflowing the annotations in a new document layout such that the annotations conform and adapt to the new layout while preserving the original intents and meanings of the annotations. A digital ink annotation system includes a classification module, an anchoring module, a reflow module and a clean-up module to implement the digital ink annotation process.