The "world that was" in 2 Pet 3 was the world before the Flood of Noah. That is the only world wide Flood that has ever occurred. The rebellion of Satan occurred during or before Adam was in the Garden, and Adam was in the Garden by the end of the 6th day. There was no Flood before that, because the waters above the Earth and the waters below the Earth were still intact while Adam was in the Garden.
That's the popular notion about 2 Peter 3, but the following is about the condition of the earth at Genesis 1:2-9 with waters overspread all of it,
"... that by the word of God the heavens were of old, and the earth standing out of the water and in the water: Whereby the world that then was, being overflowed with water, perished:" The phrase,
"by the word of God the heavens were of old", is about Genesis 1:1 when God first created the heavens and the earth in the beginning. Peter is actually revealing 3 world earth ages:
1. "the world that then was"
2. "the heavens and the earth, which are now"
3. "new heavens and a new earth"
Per Ezekiel 28 God gave a parable where He uses the prince and king of Tyrus to point to Satan. He showed that He originally created Satan perfect in his ways, before iniquity was found in him, and he rebelled in coveting God's throne. That was in that 'world that then was' when Satan was perfect and followed God at His Altar as the anointed cherub that covereth. And of course that was way... before Adam and Eve. By the time Satan shows up in God's Garden as 'that old serpent', tempting Eve, he had already rebelled long before that and was established as the tempter and adversary.
You are correct that the Flood did not literally destroy the Earth, but it did destroy all land animal life on Earth at the time.
God's consuming fire will literally exterminate all matter, time, space, energy: everything that is the physical universe. It will not become a "Sci-Fi movie asteroid belt". It will cease to exist. And a new heaven and Earth will be created in its place.
God's consuming fire will not literally destroy the whole earth, but will only wipe its surface. Per the 7th Trumpet of Rev.11, when Jesus returns, which will be the "day of the Lord" when 2 Peter 3:10 is to happen, notice that Rev.11 Scripture says that all the kingdoms of this world then become the kingdoms of The Father and His Son. Where do you think those kingdoms will be when Jesus takes reign, in outer space? No, of course not, that's a silly idea.
And if space were destroyed at that event, where would Jesus and His reign over the nations from? Like I said, you shouldn't just throw away that Zechariah 14 chapter which is about the time of Christ's future coming on the "day of the Lord", and thereafter with His future reign over the nations upon this still existing earth.
The things that can be shaken in Heb 12:25-29 are the things of this creation. The things of the spiritual realm are the things that cannot be shaken. The Kingdom of God, which is a spiritual kingdom not of this world, cannot and will not be shaken. But everything that is of this creation, not only the Earth, but also the first two heavens (sky and "space") will not only be shaken, but completely removed.
The things shaken Paul points to are man's works, which is what Apostle Peter pointed to being burned up in 2 Peter 3:10. Also, the word "
elements" in 2 Peter 3:12 does not mean earthly matter. It is the Greek word
stoicheion, which means 'an orderly arrangement, a serial' (NT:4747). It is pointing to a world order, i.e., this 2nd world earth age time.
And when Paul in Hebrews 12 quoted God as saying, "Yet once more, I shake not the earth only, but also heaven", God was pointing to a previous time when He shook this old earth, and it was not at the flood of Noah's day. It was long before Noah, and even long before Adam and Eve. It was when Satan first rebelled, and God ended that 1st world earth age. If you don't understand this, then you won't understand God's parable about Satan in Ezekiel 28, nor Isaiah 14, and definitely not what Apostle Paul taught in Romans 8:18-25 about God having placed today's present creation in bondage to corruption. The Jeremiah 4:23-28 Scripture will also be a mystery to you.
Even the following point you will have missed...
Zech 14:1-3
14 Behold, the day of the LORD cometh, and thy spoil shall be divided in the midst of thee.
2 For I will gather all nations against Jerusalem to battle; and the city shall be taken, and the houses rifled, and the women ravished; and half of the city shall go forth into captivity, and the residue of the people shall not be cut off from the city.
3 Then shall the LORD go forth, and fight against those nations, as when he fought in the day of battle.
KJV
Modern Bible versions try to remove the past tense of that above "as when he fought in the day of battle" phrase. Even the NKJV changed it.
But what previous battle is that pointing to that Christ fought before this event of His 2nd coming here? Some try to say it was against Pharaoh and his army, but that's a small army compared to this battle against the nations gathered against Jerusalem on the last day, which is what timing this Zechariah 14 event is pointing to.
The previous "day of battle" being referred to that Christ fought was about the time when Satan and his angels rebelled against God in that old world. Rev.12:3-4 reveals that Satan had a previous beast kingdom of ten horns, seven heads, but only seven crowns when one third of the angels ("stars") rebelled with him in that 1st world earth age. The beast kingdom of Rev.13:1 is to have ten crowns instead and is for the very end of this world.
So if you don't understand about that 1st world earth age before Satan rebelled and thereafter, then you will have missed many Truths in God's Word.