Gerry McGowan, Michael Toner, Stephen Crumlish and Gerard Kelly were all teenagers when they were accused of killing Lt Steven Kirby in 1979.
The so-called Derry Four fled Northern Ireland until their acquittal in 1998.
They are now involved in a civil case against the police for wrongful arrest.
They four men also say they were subjected to false imprisonment, assault, battery and malicious prosecution.
The PSNI told the BBC it would be inappropriate to comment due to legal proceedings.
On Friday, lawyers for the PSNI chief constable submitted documents to the High Court in Belfast indicating that all original interview notes from 1979 were missing.
"I suppose my first reaction was one of disbelief but at the same time it was not surprising," said Gerry McGowan.
"These documents could have been forensically tested to determine whether the statements were tampered with.
"Were they wilfully destroyed or was it just complete incompetence?"
It is understood that no explanation was provided as to how the notes had gone missing.
It is yet another twist in a long battle for justice, according to Paul O'Connor from the Pat Finucane Centre.
"It is an incredible coincidence that in this particular case the interview notes have gone missing," he said.
"It would be vital to get to the bottom of this to see what was written in the original interview notes and this is quite a blow for them.
"My heart goes out to the four men, clearly they have been vindicated in terms of having the charges withdrawn but they've had no justice."
The four men have now lodged an application for the release of covert tape recordings of the interviews, which they believed were made by the security services.

Some of the men come from families with close links to the government. One has escaped from custody.
The victim, Zouhoura, is the daughter of an opposition leader and was threatened with death if she spoke about the attack.
A video of her rape sparked a wave of protests in Chad in February.
Africa Live: More on this and other news stories

The Manx rider, 24, finished 22nd on the final time trial to top the general classification by 12 seconds ahead of his Team Sky team-mate Dario Cataldo.
Cataldo won the final day's 10km individual time trial to make it a one-two for the British team.
It's like being in dreamland. To win four out of five stages is not a common thing to do but the team was super strong this race
The victory is the Isle of Man cyclist's first stage-race triumph of his professional career.
He later said on Twitter: "Was a nervous time trial yesterday with my tri bars coming loose but nice to finally finish it off and also have Dario on the podium with me."
The British team dominated the race after Isle of Man-based Ben Swift won the opening stage on Thursday before a quartet of Team Sky riders won the afternoon's time trial.
Kennaugh recorded the first stage win of his career on Friday and the Manxman did not relinquish the leader's jersey.
Team Sky director Dan Frost said: "It was a perfect end to a perfect week for us.
"It's like being in dreamland. To win four out of five stages is not a common thing to do but the team was super strong this race.
"Now having Dario win the trial and to move up to make it a one-two overall is also a really nice result. We won the points jersey with Swifty, the team classification and it was really nice to see Pete take the overall.
"It is great for morale going forwards."
One of four men wrongly accused of murdering a British soldier has said he is "devastated, but not surprised" to learn that interview notes relating to the case have gone missing.
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Seven men have been sentenced to 10 years for the rape and kidnapping a schoolgirl in the Chadian capital, Ndjamena.
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Peter Kennaugh recorded a landmark overall victory at Settimana Coppi e Bartali in Italy on Sunday.