God doesn't lose independence by manifesting everything. Kṛṣṇa, the Supreme Personality of Godhead, said in Bhagavad-gītā,

BG 7.12: Know that all states of being — be they of goodness, passion or ignorance — are manifested by My energy. I am, in one sense, everything, but I am independent. I am not under the modes of material nature, for they, on the contrary, are within Me.
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