If a document without an new line after %%EOF was signed incremental, the first object in the revision will be wrote directly behind the %%EOF without a blank or a new line
this will look like this:
%%EOF1 obj <<......>>
The adobe reader can read such documents, the pdfbox skip it. I looked inside the pdf specification and can't find more details about such kind of documents, so I think this is a valid document. In case that some readers can handle it, I added a "new line" before writing the incremental update with the PDDocument.saveIncremental method.