Is it permissible to worship through the Hizb al-Bahr of the Sufi al-Shadhili, or to commit to reciting it daily after the 'Isha prayer, for protection and purification of the soul, despite the presence of incomprehensible phrases within it?

It is not permissible to worship Allah through innovated "hizbs" (liturgies/parties) because they are innovations in religion. The prohibition becomes more severe if they contain incomprehensible phrases or anything that is rejected by Islamic law. Ibn Taymiyyah was asked about someone who says: "Ya Arzan, Ya Kiyan"; he replied that this was not narrated from the Companions, nor the Salaf, nor the Imams, and these words have no meaning in the Arabic language. Any unknown name, no one is permitted to use it for ruqyah (exorcism/healing) or supplication. Goodness and blessing lie in adhering to what has been authentically established from the Messenger of Allah, may Allah's peace and blessings be upon him.