Will the disobedient son be held accountable for his disobedience towards his father, or will he not be held accountable given that he is repaying his disobedient father for his own disobedience towards his father?

There is no Shar'i (Islamic legal) evidence linking parental disobedience ( 'uquq al-walidayn) with the punishment of children being disobedient to their parents. However, it has been narrated in a hadith that has been graded as both hasan (good) and da'if (weak): "Be dutiful to your fathers, and your sons will be dutiful to you." The understanding derived from this is that whoever disobeys their parents might experience disobedience from their own children. Recompense is of the same nature as the deed, but this is not absolute. Parental disobedience is among the grave sins ( al-mubiqat), and Allah may delay its punishment. A dutiful child may be afflicted with disobedient children due to divine wisdom. The disobedience of children towards their parents (even if the father had been disobedient to his own parents) does not absolve them of responsibility, because they transgressed Allah's command by their own free will, and "every soul, for what it has earned, will be retained."