It would help if you gave us a small, working example that we can actually run and debug.

But it might be easier if the functions wouldn't assign stuff to a hash ref, but return a value, which the caller can then assign, ie you write something along these lines:

$EDHRef->{$key} = extractDataFunctionHash{$key}->($key, $DNRef);
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That way it's much simpler to debug.

One (possibly unrelated) thing to be aware of is this: $EDHRef->{$key} = \@extractedLinesArray; If @extractedLinesArray is not locally scoped to the current sub, it will always assign a reference to the same array, so all the values in %$EDHRef will end up being the same array.