After embedding of the preflight results the PDF is “sealed” with a digital signature. The content of the PDF remains unchanged at least with Acrobat 9 to XI.
Acrobat DC now changes the PDF version to 1.6. This means that a valid PDF/X-1a document (PDF 1.3) which does not create any error with a PDFX-ready preflight profile V1.3, generates an error “PDF version is newer than 1.3” when checked again with the same profile. That’s not good and confuses a lot of users!
PDF/X-4 files are not affected since PDF 1.6 is allowed in PDF/X-4.