How to identify possible false negatives in labels?
I think your problem is not with identifying the false negatives, it's with defining the classification problem properly.
If I try to phrase what you're trying to predict, it would be something like this: &quot;Given the data about a drilling point, what's the probability of encountering a difficulty up to depth $x$&quot;.
So, if you have a hole which didn't reach that depth $x$, it's not a false negative - it's just a missing label (no test... yet).
If you want to make your prediction based on the information known before drilling (or, at least, before drilling up to a given depth $z$) - limit your model to that information.