I can understand your concerns.
In just born babies, any infection is to be taken seriously as it may spread to the brain and blood easily as you have been informed by your doctors.
And yes sometimes, LP is not successful in small babies.
Since already antibiotic has been started, you need not worry as it will take care of the infection.
If baby is not responding to antibiotics, doctors will take further decisions... like repeat LP. Also blood tests like Complete blood count
, CRP etc will help them to understand the infection.
So do not worry. Follow your doctor`s advice.
Wish a speedy recovery for your nephew.