Ihave PDF file which was signed by some other application. When I try to sign it with PDFbox, previous revision is damaged. I have discussion at stackoverflow, with Michael Klink.
when we see some changes merely was structural. Some changes was just rounding problem -
When I test, problem of damaged signature was caused from structural change [when there must be direct reference, there was indirect reference and etc..]
So we solve that problem. I will upload damaged PDF document, fixed pdf, and the patch too.