From rare parchments and ancient Egyptian mummies to artworks including a Rembrandt and a prized Leonardo da Vinci portrait, the Czartoryski collection, added to by generations of Polish nobles, is one of the most intriguing and varied in Europe.

Its fate has been a mirror of Polish history: begun in lieu of a national museum at a time when Polish independence was under threat, it was taken to Paris when the country disappeared from the map in the 19th century. Parts were later seized by the Nazis, then grabbed back by the Soviets.

The chequered story has continued into the present and a bitter dispute is currently ongoing over a €100m (£86m) deal in which the Polish state bought the collection from the heir of the Czartoryski family, who was raised in Spain and does not speak a word of Polish.

But after a decade-long closure for renovations and expansion to the museum that houses it, the collection is now back on display in Kraków. The refurbishment has updated the museum and doubled the exhibition space, so that over two floors visitors can view a unique representation of European culture and history, and Poland’s place within it.

“It’s like Noah’s Ark. It had to be taken through the difficult periods of partitions and preserved for the future, when we would regain our independence,” said Andrzej Szczerski, the director of Kraków’s National Museum, which includes the entire Czartoryski collection after the state’s purchase of it in 2016. It includes 86,000 objects and a library of 250,000 books and manuscripts, many of key historical importance.

When describing the collection, Princess Izabela Czartoryska, who began to amass it in the early 19th century and put it on display at the family estate, said: “My homeland, I was not able to save you, let me immortalise you at least.”

In pride of place at the new museum is Leonardo’s Lady with an Ermine, one of just four portraits of women by the master. Dated to around 1490, it depicts Cecilia Gallerani, the young mistress of Duke Ludovico Sforza of Milan, a patron of Leonardo.

Facebook Twitter Pinterest It is estimated that Leonardo da Vinci’s Lady with an Ermine is probably worth more than €100m alone. Photograph: Carl Court/Getty

It was bought in 1798 in Rome by Prince Adam Jerzy Czartoryski, Izabela’s son. The foreign minister to the Russian tsar, he later became a critic of Russia after the partitions of Poland, and lived out his life at the Hotel Lambert in Paris, a mansion that also housed the art collection for decades. It was returned to Poland in 1876 and put on display in Kraków, where it bore witness to the continuing troubles in the country’s history.

Hans Frank, the Nazi governor of Kraków, took the Leonardo and several other paintings with him when the Nazis retreated. After his arrest at the end of the war, it was discovered by allied soldiers, who returned the painting to Kraków.

Now it is displayed in a separate room in the museum, and offers a rare chance to see a Leonardo without thronging crowds. Also on display are ornate medieval ivory carvings, jewelled peacocks, vases and tapestries, as well as a large collection of Polish royal portraits, armour and memorabilia from over the centuries.

“This collection represents a unique vision of European culture, Polish culture within it, and as a result I find it more interesting than a standard collection full of masterpieces,” said Szczerski.

Adam Karol Czartoryski, who was born in Seville shortly after his father escaped Poland in 1938, was the legal heir to the collection as the great-great grandson of Adam Jerzy. In 2016, he negotiated the €100m sale with culture minister Piotr Glinski from Poland’s ruling Law and Justice party, who has been accused of meddling in the nation’s cultural and museum life on multiple occasions.

In June 2016 Glinski wrote to Czartoryski with an offer to buy the collection, but in order to sell it, the prince needed the approval of his foundation’s board.

Marian Wolski, an art historian who was head of the board at the time, said there was no justification for the state to pay so much for a collection that was already forbidden from being taken out of the country. “I did not want to be enmeshed in this swindle in any way,” said Wolski, who resigned along with his deputy. “This is a place where two cardinal sins met: greed and hubris.” A hastily convened new board quickly inked the deal.

Wolski said Czartoryski had initially wanted the money to go to his private account, but this was not countenanced by the Polish government, who would only pay the money to the foundation on the basis that it would be used to continue funding Polish cultural initiatives. The money has since been moved to Lichtenstein, which has only made sceptics of the deal more suspicious.

Maciej Radziwilł, the current head of the board and himself part of the Czartoryski family, said the prince had not touched the money for his personal use, and that the foundation could account for every cent. “It’s a shame this huge achievement has been tainted by scandal. A minister of culture in the UK would probably have been given a medal from the Queen for buying a collection like this for 5% of its value,” he said.

Szczerski dismissed the critics, saying it was a “historic and fantastic moment”. Now the collection is back on display, he said, one major mystery remains to be solved: the fate of the Portrait of a Young Man, by Raphael. Looted by Hans Frank, along with the Leonardo, it was never found after the war. However, Szczerski said he had been told by people in the art world that they believe they have traced the painting to a private collection.

He declined to give any more information about where the intelligence led, but said the Polish state was very interested to recover it and would begin to take steps to do if they could confirm the information. He also called on the family he believes is in possession of the painting to return it voluntarily.

“Someone has to make a moral decision and acknowledge that their forefathers took it, and return it,” he said.