Certain combinations of documents don't retain tags when merged. The document Tagged.pdf is just a basic one word PDF created and tagged with Pro DC. If you try to merge this with the government General Forbearance form the output crashes DC when you try to view the tags. If you use a flattened version of the General Forbearance form then the tags are just munged.
The included patch appears to make tagging more reliable, but I'm still relying heavily on cloning which can apparently cause other issues. The documents I get out with this code seem present correctly in Adobe readers for all combinations of documents that I tested against.
My patch is made and tested against yesterdays production head and it includes my changes from PDFBOX-3999 since it is in the exact same place in the code.
The priority of this is a blocker for 508 compliance of merged documents but I guessed it to be more of a minor issue in the overall scheme of things, please correct me if I am mistaken.