It seems that Sir Humphrey Clones are still there.

 On Wednesday the Guardian reported that

It is deeply concerning, therefore, to discover that about 1,000 files have gone missing after being removed by civil servants. Officially, the archives describe them as “misplaced while on loan to a government department”.
The files, each containing dozens of pages, cover subjects such as the Troubles in Northern Ireland, the British colonial administration in Palestine, tests on polio vaccines and territorial disputes between the UK and Argentina. It is unclear whether duplicates exist.
The loss of so many documents of such significance has understandably caused concern among historians, politicians and human rights groups. Amnesty International has called on Theresa May to order an urgent government-wide search for the documents, while Labour MP Jon Trickett has warned that the loss “will only fuel accusations of a cover-up”.
Such suggestions may seem far-fetched, but recent history has given many people reason to be suspicious. Documents in the National Archives have previously been key in revealing human rights abuses by the British state.
In 2014, for instance, investigators from the Irish broadcasterIn 2014, for instance, investigators from the Irish broadcaster RTÉ uncovered a 1977 letter from the then home secretary, Merlyn Rees, to the prime minister of the day, James Callaghan, in which Rees claimed that ministers had given permission for torture to be used in Northern Ireland during the Troubles. The information had reportedly been withheld from the European court of human rights.

Also in 2014, the government was accused of a cover-up after it said it could not release information about the CIA’s “extraordinary rendition” programme because the files had suffered “water damage”

 I wonder how long this has been happening because  "The Skeleton in the Cupboard" isthe seventeenth episode  of Yes Minister  first broadcast in 1982and contains  the following conversation between Minister Jim Hacker and Permanent Secretary Sir Humphrey Appleby 

Sir Humphrey Appleby: Well, this is what we normally do in circumstnces like these.
James Hacker: [reads memo] This file contains the complete set of papers, except for a number of secret documents, a few others which are part of still active files, some correspondence lost in the floods of 1967...
James Hacker: Was 1967 a particularly bad winter?
Sir Humphrey Appleby: No, a marvellous winter. We lost no end of embarrassing files.
James Hacker: [reads] Some records which went astray in the move to London and others when the War Office was incorporated in the Ministry of Defence, and the normal withdrawal of papers whose publication could give grounds for an action for libel or breach of confidence or cause embarrassment to friendly governments.
James Hacker: That's pretty comprehensive. How many does that normally leave for them to look at?
James Hacker: How many does it actually leave? About a hundred?... Fifty?... Ten?... Five?... Four?... Three?... Two?... One?... *Zero?*
Sir Humphrey Appleby: Yes, Minister.

It was clear over 30 years ago  that the writers Anthony Jay and  Jonathan Lynn had a deep insight into the machinations of government  and that notjing has changed.