I may be misunderstanding how all this works.
If there are bad PDFs, the scheduled task \assignfeedback_editpdf\task\convert_submissions might encounter one of the many thrown errors such as "Unable to find pointer to xref table". My understanding of the conversion script is that it will attempt items in the queue 3 times (default setting) and then remove an item that can't be converted from the queue. Some of the errors that occur, such as "Could not find readonly pages for grade $grade->id" seem to allow the script to continue but others, such as the "unable to find pointer to xref table" do not.
It seems to me that corrupted PDFs should never stop the conversion script. It should just remove those from the queue and carry on. If instructors see corrupted files in their student's assignment submissions, they can talk to the student about it.