Just like the souls merge into the body of Lord Viṣṇu at the end of each day of Brahma, and also after the final dissolution of the universe, the soul goes to the small space inside the heart to meet the Lord in His form as Paramātmā at the end of each day, during deep sleep. Being the eternal part and parcel of the Lord, the soul can't remain separated from Him. Thus, at the end of each cycle of material activity (at the end of each day, at the end of each day of Brahma, and at the end of the life of Brahma, when the universes are destroyed), the soul merges into the body of the Lord.
What makes this merging different from liberation is that during this encounter with the Lord in the conditioned state, the soul is forgetful of his eternal relationship with Him, and still contaminated by the false ego and material desires. The soul thus doesn't associate with the Lord during these encounters, but just remains in an unconscious state, in a kind of deep slumber. When the soul wakes up at the beginning of the next cycle, the soul remembers his material desires and thus becomes again busy performing different material activities to try to satisfy them.
Going back to Godhead, on the other hand, means that the soul not only becomes free from all material desires as well as the false ego but is able to awaken his real spiritual nature, including his spiritual body and senses, with which he can enter the spiritual planets and personally associate with the Lord.
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