Correct grammar for "due to" in the past
Solution 1:
As this answer says, the second version is wrong. It would also be wrong to use the first, because it has problems which you can avoid by recasting part of it.
One problem is not related to the use of "due to". Consider this extract:
By the time the rescuers arrived, which took a long time, they had only eaten 2 peanuts each.
The time the rescuers arrived didn't take a long time --- that's absurd. Perhaps the rescuers' journey took a ling time; perhaps the rescuers departed late. Anyway, the last clause indicates that the pertinent matter is the time the rescuers arrived. So let's recast:
By the time the rescuers arrived, which was late, they had only eaten 2 peanuts each.
Someone who knows more about the story might be able to do better, but this is the best I can do with the information in the OP. The pronoun "they" also needs clarifying. Obviously the parsimonious peanut-eaters are the people rescued, but the sentence makes it refer to the rescuers. So the peanut-eaters need an explicit mention here.
Now let's deal with the "due to" phrase. You could say that the rescuers' late arrival was due to the helicopter problem. The sentence as I recast it mentions the late arrival time but not the late arrival itself. But we don't have to use "due to". we can link clauses in a different way, thus:
By the time the rescuers arrived, which was late because the helicopter was unable to take off, they had only eaten 2 peanuts each.
Using "due to" entails saying something like this:
The rescuers' late arrival was due to the helicopter being unable to take off.
This can't be fitted elegantly into a matrix of the form "By the time X happened, Y had happened". This is the best I can do, working with the added constraint to keep the punchline last:
By the time the rescuers arrived (their late arrival being due to the helicopter being unable to take off), N and N had only eaten 2 peanuts each.
Solution 2:
In 19th century formal grammar, you would have had to say
due to the helicopter's not being able to lift up ...
Today, that is the more formal and less common version, and the more usual version is
due to the helicopter not being able to lift up ...
Both versions are perfectly fine, although for the most formal writing, it's possible you want to use the possessive version.
The "correct version" people told you to use is wrong. Possibly what they were telling you to use is
due to the fact that the helicopter was not able to lift up ...
Personally, I dislike the phrase "the fact that" and try to avoid it when I can (although sometimes it is necessary because of grammar).
Finally, "lift up" is not a very idiomatic phrase here, even though it's grammatically correct. I would suggest using either "take off" or "gain altitude", depending on the meaning.
Solution 3:
Actually, the first sentence (yours) is completely correct, grammatically. Honestly I don't know much about how exactly grammar works but why I feel this is correct is because "not being able to lift up" is not a helicopter's property or something. If you want to use "helicopter's" you can say "due to the helicopter's weakness on lifting up". again, I'm not sure if this is correct or not since I'm not an English native speaker.