Material time is continuously "moving" from past, to present, to future for infinity in the constant cycles of material creations and annihilations.

This flow of time means material energy is in a constant state of decline and decay -from birth, youth, middle age, old age and death.

The individual material universes, known as Brahmandas, are coming from the body of Maha-Visnu. 

They are all governed by the flow or movement of material time - past, present and future, unlike the "eternal presence" of time in Vaikuntha and Goloka-Vrindavana, the Kingdoms of God.

Therefore, when Maha-Visnu breaths out, gradually all Brahmanda universes begin to manifest, but when He breaths in, some are destroyed while others are "in line" to be destroyed within the movement of time.

It all does not happen at once.

Remember material time means "moving" from past, to present, to future. 

The Brahmanda universes are also constantly coming from the pores of Mahā-Viṣṇu's skin, which is a constant flow in both directions at different stages of time.

Each Brahmanda universe has a secondary inner material universe within it created by Garbhodakashayi Visnu and managed by Brahma.

Both the Brahmanda universes and their inner secondary universes lasts for the same life span of Brahmā, which is 311 trillion and 40 billions human years. 

According to Srimad Bhagavatam there is silence in ONLY that part of the material creation experiencing annihilation (not all material worlds at the same time) for another 311 trillion and 40 billion years. 

Other Brahmanda universes are going on in their time zone during that annihilation (Maha-Visnu breathing in)

In other words the entire material creation does NOT shut down all at once.

Also the jiva-souls have existed for "infinity" which means they are beginningless and endless.

Bhagavad Gita As It Is 1983 correct edition, Chapter 2 text 12-

"Never was there a time when I did not exist, nor you, nor all these kings; nor in the future shall any of us cease to be." (BG Ch 2 text 12)

Bhagavad Gita As It Is 1983 correct edition, Chapter 2 text 20-

"For the soul there is neither birth nor death at any time. He has not come into being, does not come into being, and will not come into being. He is unborn, eternal, ever-existing and primeval. He is not slain when the body is slain." (BG Ch 2 text 20)

Please avoid reading Prabhupada's incorrect 1972 edition of Bhagavad Gita As It Is where the above text indicates the jiva-soul has a beginning when it is beginningless.**