For years, as the government has declassified and published documents related — some very tenuously — to the assassination of President John F. Kennedy, the assumption expressed by conspiracy theorists and some historians was that anything still being withheld could be big.

That assumption led some of President Trump’s allies, including Kennedy’s nephew, Robert F. Kennedy Jr., who is now the nation’s top health official, to push him to release the final tranche of files from the Kennedy archives, believing they might reveal damning evidence: namely, that Kennedy was not assassinated by a lone gunman in Dallas.

But with the release of nearly 64,000 pages by the National Archives over the past 24 hours, including some that previously included redactions, it is becoming clear that something else might have been behind the secrecy: protecting the sources and occasionally unsavory practices of U.S. intelligence operations.

The documents are still being reviewed, so there could still be major revelations ahead, though historians consider that highly unlikely.

But judging by one standard — reviewing previously released items that are no longer redacted — the real concern appeared to be that this tranche would provide friend and foe alike the names of still living C.I.A. agents and informants, intelligence-gathering operations directed at allies, covert operations and even C.I.A. budgets.

Case in point: files detailing how the C.I.A. was gathering clandestine information in Cuba. One example comes from a presidential intelligence memo dated Nov. 23, 1963, the day after Kennedy was killed, and presumably addressed to the new president, Lyndon B. Johnson.

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