PDFBOX-3540 the detection of a linearized file which has later been updated for PDF/A validation was improved so that provisions can be properly applied or ignored. That could be improved by checking the /L entry of the linearization dictionary. The ISO 19005-1:2005/Cor.2:2011 has this:
In a linearized PDF, if the ID keyword is present in both the first page trailer dictionary and the last
trailer dictionary, the value to both instances of the ID keyword shall be identical.
This provision shall not apply where the value to the L key in the linearization dictionary does not match the actual length of the PDF.