After merging two tagged documents, closing the source document causes the destination document to be closed, which prevents it from being saved. The following code demonstrates the bug with the attached flattened government PDF file. The original is available here if you need it.
The issue is resolved with the attached patch.
Also I removed the "if (mergeStructTree)" is because mergeStructTree is always true here because this code is already inside an "if (mergeStructTree)".