Firstly, Not only Adi Shankara but Sri Madhusudana Sraswati too, in the Advaita Siddhi, refuting the claims of the Dvaitin, concludes:
[Pariccheda 2, p.745 of the Edition published by MM Ananthakrishna
Shastry]:
//etena bhagavallokaaderapi nityatvam apAstam. Na cha ‘ato hi
vaiShNavA lokAH nityAste cetanAtmakaaH. matprasAdAt parAm shAntim
sthAnam prApsyasi shAshvatam’ ityAdyAgamavirodhaH, tasya
avaAntarapralayasthatvaparatvAt. TasmAt nirguNam nirAkAram brahma iti
siddham. Iti advaita siddhau brahmaNo nirAkAratva siddhiH//
[Thus (in view of the foregoing arguments), the ‘eternality’ of
divine/lordly/worlds too stands negated. One aught not to raise an
objection that the following scriptural passage is contradicted by the
above conclusion: ‘Therefore indeed the VaishNava loka-s are eternal
and are sentient in nature. By My grace you shall attain the state of
great and eternal peace.’ The ‘eternality’ stated in this passage has
its purport in the ‘avAntara pralaya’, intermediary dissolution. Thus
stands established that Brahman has no form in the work called
‘Advaita siddhi’.]
Secondly, Adi Shankara was a nondualist who ascribed nityatva (eternality) to nothing other than Nirguna brahman while all Vaishnava philosophers are dualistic who believe in the eternality of the Saguna form and Loka of God and see the concept of absolute unity (in the Advaita sense) itself as false. So there is no point in attempting to 'reconcile' Adi Shankara's statements with the philosophy of a Rival school.
As far as the Vaishnavite stance on Adi Shankara is concerned, Vaishnavas simply believe Adi Shankara's philosophy itself to be false on the basis of Padma Purana, Uttara khanda chapter 236.
The doctrine of Māya (illusion) is a wicked doctrine and said to be
pseudo-Buddhist. I myself, of the form of a brāhmaṇa, proclaimed it in
Kali (age). 8-12. It shows the meaninglessness of the words of the
holy texts and is condemned in the world. In this (doctrine) only the
giving up of one’s own duties is expounded. And that is said to be
religiousness by those who have fallen from all duties. I have
propounded the identity of the Highest Lord and the (individual) soul.
I stated this Brahman’s nature to be qualityless. O goddess, I myself
have conceived, for the destruction of the worlds, and for deluding
the world in this Kali age, the great doctrine resembling the purport
of the Vedas, (but) non-Vedic due to the principle of Māya (illusion)
(present in it).
So from the above, the only "explanation" of it as per a Vaishnava perspective would be that he said so to cause delusion
Of course, the validity of the above Purana statement itself can be critiqued on several grounds, but I won't be going into them, since that is not the subject of the question