Hi, I tried to sign up for JIRA but was denied. I'll upload the code + PDF files there once you approve it.
--- I have an FDF file containing an Acrobat "sticky note", which consists of two annotations: text (2 0 obj) and popup (3 0 obj). The annotations reference each other. The text annotation's "/Popup 3 0 R" references the popup annotation. The popup's "/Parent 2 0 R" references the text annotation. 2 0 obj <<... /Popup 3 0 R ...>> endobj 3 0 obj <<... /Parent 2 0 R ...>> endobj Now I add those annotations to an existing PDF. IDs 2 and 3 are already in use so pdfbox assigns them some new available ID. Expected Behavior In pdfbox 2.0.30, the object are reassigned to some available ID: 38 0 obj << ... /Popup 39 0 R ... >> endobj 39 0 obj << ... /Parent 38 0 R ...>> endobj Actual Behavior In pdfbox 3.0.0, the objects are assigned a new ID but their references are unchanged, so the /Popup and /Parent reference some other arbitrary object: 3473 0 obj << ... /Popup 3 0 R ... >> endobj 3474 0 obj << ... /Parent 2 0 R ...>> endobj -- Derek Wickern