If you clearly read full Vishnu Sahasranama Bhasya of Adi Shankara, then it is clearly seen that he holds Hari Hara Abheda. Some points which I also discuss in my answer here.
While commenting on the name 'Shiva', Shankara cites Kaivalya Upanishad verse 'He is Brahma.. He is Shiva.. He is Indra'
And while commenting on the name Rudra, he cites a verse from Shiva Purana which states Shiva is Parama Karanam.
'रुर्दुःखं दुःखहेतु वा तद्रावयति यः प्रभुः ।
रुद्र इत्युच्यते तस्माच्छिव परमकारणम् ।।'
"Ru means suffering and cause of suffering and Lord is the remover of that. Thus he is called Rudra and thus Shiva is the Parama Kaaranam (Supreme cause)."
And most importantly in the beginning part of Vishnu Sahasranama he cites verse from Harivamsa, which is statement of Shiva:
नामानि तव गोविन्द यानि लोकेमहान्ति च ।
तान्येव मम नामानि नात्र कार्या विचारणा ।। (Harivamsha 3.88)
Oh Govinda your names which are famous in this world, these are also my names there is no doubt in it.
He also cites Vishnu Purana verse where Krishna speaks to Mahadeva as:
त्वया यदभयं दत्तं तद्दत्तमग्विलं मया ।
मत्तो विभिन्नमात्मानं द्रष्ट्रं नार्हसि शंकर ।।
योऽहं स त्वं जगच्चेदं स देवासुरमानुषम् ।
अविद्यामोहितात्मानः पुरुषा भिन्नदर्शिन ।।(Vishnu Purana 5.33.47-49)
That Abhaya which was given by you was also given by me. Oh Shankara do not see yourself different from me.That which is me the same is you, this entire creation, Devas, Manyushyas and Asuras. Only those who are deluded by Avidya see me and you as different.
And he also cites warning of Maheswara from Harivamsha in his Bhasya:
विष्णोरन्यं तु पश्यन्ति ये मां ब्रह्माणमेव वा ।
कुतर्कमतयोमूढा पश्यन्ते नरकेष्वध ।।
ये च मूढा दुरात्मानो भिन्नं पश्यन्ति मां हरे ।
ब्रह्माणं च ततस्तस्माद् ब्रह्महत्यासमं त्वधम् ।।
He who sees myself and Brahma different than Vishnu, such fools surely fall in hell. That Durãtmãn who sees myself different from Hari does a sin equivalent to BrahmaHatya.
Thus, it is clearly seen Adi Shankara strongly hold Hari Hara Abheda and as per Shankara those who differentiate between Hari and Hara are doing sin equivalent to BrahmaHatya.