Cycles of universal destruction: How not everything is destroyed at the end of the day of Brahma
We hear that the universe is destroyed at the end of each day of Brahma and recreated at the beginning of the next day. This is only partially true. In reality, most of the universe survives.
It's described in the Srimad Bhagavatam that Brahma used the material elements from the Lotus flower he was born from to create fourteen planetary systems:
1) Satyaloka,
2) Tapoloka,
3) Janaloka,
4) Maharloka,
5) Svargaloka,
6) Bhuvarloka,
7) Bhūrloka (of which our planet is part),
8) Atalaloka,
9) Vitala-loka,
10) Sutala-loka,
11) Talātala-loka,
12) Mahātala-loka,
13) Rasātala-loka,
14) Pātāla-loka.
The planetary systems of Atala, Vitala, Sutala, Talātala, Mahātala, Rasātala and Pātāla are the lower planets, where the demons live. The Earth as well as the other planets that form Bhūrloka are called the intermediate planetary system, while Svargaloka is the higher planetary system where the demigods live. Bhūrloka is the place for Rakshasas and other subtle beings led by Kuvera. They are in the middle, considered higher than human beings, but lower than the demigods.
All these different planetary systems are destroyed at the end of each day of Brahma and recreated at the beginning of the next day.
Still higher are Satyaloka (the planet of Brahma), Tapoloka, Janaloka, and Maharloka, inhabited by great sages. These sages are in general above the feuds between demigods and the demons and engage their time in advanced devotional service. Because of that, these planetary systems are not destroyed at the end of the day of Brahma, surviving until the end of his life.
Svargaloka, Bhuvarloka, Bhūrloka, etc. are not single planets, but planetary systems which include a number of planets each. The Earth, for example, is part of Bhūrloka, a planetary system that includes all the different structures that Srimad Bhagavatam describes as part of Bhu-Mandala. Although for the demigods these structures appear to be observable as a series of concentric islands, for us, they appear as different planets.
The inhabitants of these different planetary systems have different levels of consciousness and as a result different sets of senses. As part of the population of Kali-yuga, our consciousness is very gross, and thus we have senses that can experience only gross matter, while demigods, demons, and other beings have more subtle senses that are able to perceive different varieties of refined matter that is not visible to us. It's interesting to note that modern theories predict that up to 95% of the universe is composed of dark matter and dark energy, forms of matter we can't detect with our senses or instruments. Higher beings with more refined senses are capable of observing all these subtle forms of matter, and thus they perceive the universe differently from us.
We like to call our perception of the universe "reality", but the way we see things is just the way our mind interprets the electrical signals that our eyes, hands, etc transmit to the brain. Other species around the universe have different sets of senses, and thus "reality" for them is something completely different.
From these fourteen planetary systems, ten are destroyed at the end of each day of Brahma, including all the lower planets, as well as the intermediate planets and the abodes of the demigods. The list includes Svargaloka, Bhuvarloka, Bhūrloka, Atalaloka, Vitala-loka, Sutala-loka, Talātala-loka, Mahātala-loka, Rasātala-loka and Pātāla-loka.
This happens because the ultimate goal of the creation of the universe is to offer an opportunity for the souls to realize their eternal relationship with Krsna. As time passes and most of the souls in these different planetary systems do not engage in devotional service as seriously as they should, Lord Ananta becomes angry and eventually destroys all these different planetary systems with the assistance of Lord Shiva. All the inhabitants of these planetary systems have to wait inside the body of Lord Garbhodakaśāyī for 4.32 billion years until the next creation.
The four highest planetary systems, Satyaloka, Tapoloka, Janaloka, and Maharloka are spared from the destruction. These planetary systems actually correspond to most of the universe.
Why only these four are spared? Srila Prabhupada explains the reason in SB 3.10.9:
"This is because of the causeless devotional service rendered unto the Lord by their inhabitants, whose existence continues up to the end of dvi-parardha time, when they are generally liberated from the chain of birth and death in the material world."
They were destroyed at the end of the first parardha, or the first half of the life of Brahma, and now they will continue to exist until the end of the dvi-parardha, until the end of the second half. At that time, these great sages will have the opportunity of going back to Godhead, together with Lord Brahma.
One interesting detail mentioned in the Brhad Bhagavatamrta is that although Maharloka is spared the destruction at the end of the day of Brahma, it becomes very hot, forcing its inhabitants to take shelter in Tapoloka, where the conditions are more favorable.
At the beginning of the next day of Brahma, when the lower planets are created again, these great sages go down in order to populate the universe, becoming the Prajapatis, the progenitors of the next generations of living beings. This process is described in the Vayu Purana (1.7.7):
pratyāhate pūrvakalpe pratisaṃdhiṃ ca tatra vai
anyaḥ pravarttate kalpo janāllokāt punaḥ punaḥ
"First, the the Kalpa ends and, subsequently, the Pratisaṃdhi end. Then, the next Kalpa begins with life imported from Janaloka. This process occurs again and again".
In other words, Brahma performs the complete creation of the universe, as described in the Srimad Bhagavatam two times, at the beginning of his life, and then on the first day of the second half. On other days, the prajapatis coming down from Janaloka take charge of repopulating the universe.
The description of the creation of the planetary systems described in the Srimad Bhagavatam, with Brahma drinking the wind and so on may sound mythological, but modern studies also conclude that there was a lot of chaos in the initial formation of the solar system, conditions that were not suitable for the existence of life. Later on, the conditions subdued with the formation of the planets and so on.
We should keep in mind that the descriptions of the Srimad Bhagavatam are given according to the sense perception of higher beings. What Brahma perceived as a strong wind could appear to be something different in our plane. However, we can understand the essence of the description, meaning that there were disturbances and it was fixed, allowing the planets to form and be gradually populated.
There are other descriptions that may sound strange at first. The Vedas mention that there are flying mountains for example. At first, it may sound absurd, until we realize that there are indeed flying mountains all over the cosmos in the form of asteroids and so on.
It's also important that the creation of Brahma doesn't happen by magic but by the manipulation of subtle potencies that result in the gradual formation and organization of the planets. That's not a process that happens from night to day. Modern science attributes the creation of the universe to the mere action of physical laws such as gravity, but the Vedas give a more complete explanation, describing the controllers behind the action of such potencies.