How do scientists reconstruct pre Cretaceous continent if all plates that are currently left are younger than Cretaceous?
You forgot about continents

First of all, it's necessary to point out the false premise in your question: It is not true that "all plates that are currently left are younger than Cretaceous".  There is a near-continuous record of rocks stretching all the way back to the Hadean Eon 4 billion years ago.  And there are older crystals called zircons that are found as inclusions in younger rocks.  

The thing is, these rocks are on land, part of continental crust. Your question seems to be unaware of the existence of  continental crust. Of course, since you're not currently sitting at the bottom of the ocean, you're on top of continental crust right now. Most of the big tectonic plates are part oceanic and part continental.

Continents have been built up little by little over geological time. Their rocks are a mixed-up jigsaw puzzle of various types and ages. It's the geologist's job to figure out how those pieces fit together.

Here's just a taste, and it doesn't even show the complexity of the puzzle in North America by a long shot:


(courtesy of United States Geological Survey, via Wikimedia Commons)

It is true that the oceanic plates are mostly destroyed by subduction, but the oceanic crust has to go beneath something, and that's often a continent. Besides, subduction helps make continents grow:


not all of the rock is subducted: some seafloor sediments are scraped off and piled against continental margins
The top layers of rock that are subducted melt, and the melted rock bubbles its way up through the overlying crust, producing plutons and volcanic arcs. Sometimes these are on continents (such as the Cascades and Andes) so their rocks directly add mass to them.
When the volcanoes are out in the ocean, the subduction process pulls them into continents and they get cemented to the edge. Sometimes they form little mini- continents (such as Japan and New Zealand).


The oldest oceanic crust currently at the seafloor is in the eastern Mediterranean. In an article in Nature Geoscience Roi Granot of Ben-Gurion University of the Negev suggests that the [Herodotus Basin] is a remnant of ancient Tethys Ocean, having formed up to 340 Ma during the Early Carboniferous period. Most oceanic crust is 200 million years old (Jurassic) or younger.  They're an important part of putting the puzzle together, but as I stated at the beginning of my answer, the geological record is much older, because of continental rocks.

Finally, there is really old oceanic crust in the form of ophiolites, which are bits of oceanic crust that have been incorporated into continents.  Since they're no longer part of the oceanic conveyor belt, some can be quite old. The oldest is about 3.8 billion years old.