On the question of the omnipotence of God/Ishwara...
It is not clear if Ishwara is omnipotent. In some places, Ishwara admits that He cannot change some things.
Bhagavad Gita
sadṛśaṅ cēṣṭatē svasyāḥ prakṛtērjñānavānapi.
prakṛtiṅ yānti bhūtāni nigrahaḥ kiṅ kariṣyati৷৷3.33৷৷
3.33 Even a man of wisdom behaves according to his own nature. Beings follow (their) nature. What can restraint do?
While commenting on this sloka, Sri Adi Shankara says -
tasmāt prakṛtiṅ yānti anugacchanti bhūtāni prāṇinaḥ. nigrahaḥ niṣēdharūpaḥ kiṅ kariṣyati mama vā anyasya vā৷৷
Therefore, bhutani, beings; yanti, follow; (their) prakrtim, nature. Nigrahah kim karisyati, what can restraint do, be it from Me (Krishna) or anybody else?
Here, we find Bhagavan himself admitting that He cannot make people act contrary to their nature. This is an example that probably shows that Ishwara is not omnipotent.
If Ishwara cannot change how people act, then Ishwara is not omnipotent and so most likely Ishwara cannot destroy soul.
Moreover, Bhagavan says this in Gita.
mamaivāṅśō jīvalōkē jīvabhūtaḥ sanātanaḥ.
manaḥṣaṣṭhānīndriyāṇi prakṛtisthāni karṣati৷৷15.7৷৷
15.7 It is verily a part of Mine which, becoming the eternal individual soul in the region of living beings, draws (to itself) the organs which have the mind as their sixth, and which abide in Nature.
The individual soul is an amsha or portion of the Supreme Self, and hence it cannot be destroyed even by Ishwara.
Also, commenting on Gita sloka 2.17, Sri Adi Shankara says -
asya brahmaṇaḥ vināśaṅ na kaścit kartumarhati, na kaścit atmānaṅ vināśayituṅ śaknōti īśvarō.pi. ātmā hi brahma
Therefore no one can bring about the destruction of this immutable Brahman. No one, not even God Himself, can destroy his own Self, because the Self is Brahman.
The last part applies to individual soul also in advaita. The individual soul is also essentially brahman, and thus cannot be destroyed even by Ishwara.
Appendix
A short discussion between Bhagavan Krishna and Utanka in Aswamedha parva of Mahabharata, that gives clues on whether Ishwara is omnipotent.
Utanka's words to Krishna
Utanka said,--'Since, though able, O Krishna, thou didst not rescue those foremost ones of Kuru's race, who were thy relatives and, therefore, dear to thee, I shall, without doubt, curse thee. Since thou didst not forcibly compel them to forbear, therefore, O slayer of Madhu, I shall, filled with wrath, denounce a curse on thee. It seems, O Madhava, that though fully able (to save them), thou wert indifferent to these foremost of Kurus who, overwhelmed by insincerity and hypocrisy have all met with destruction.'
Essence of Krishna's response -
In every Yuga I have to repair the causeway of Righteousness, entering into
diverse kinds of wombs from desire of doing good to my creatures. When, O son of Bhrigu's race, I live in the order of the deities, I then verily act in every respect as a deity. When I live in the order of the Gandharvas, I then, O son of Bhrigu's race, act in every respect as a Gandharva. When I live in the order of the Nagas, I then act as a Naga, and when I live in the order of Yakshas or that of Rakshasas, I act after the manner of that order. Born now in the order of humanity, I must act as a human being. I appealed to them (the Kauravas) most piteously. But stupefied as they were and deprived of their senses, they refused to accept my words. I frightened them, filled with wrath, referring to some great fear (as the consequence of their slighting my message). But once more I showed themselves my usual (human) form. Possessed as they were of unrighteousness, and assailed by the virtue of Time, all of them have been righteously slain in battle, and have, without doubt, gone to Heaven