The problem is that
```C++
acceptNoDaughters
```
explicitly needs to be set to
```C++
true
```
when running over pruned GenParticles. With
```C++
if( aParticle.numberOfDaughters() >= 0 && isAParton ) {
```
instead of
```C++
if( ( aParticle.numberOfDaughters() > 0 || acceptNoDaughters) && isAParton ) {
```
things are completely transparent to the user and there is no need to introduce any additional parameters when using pruned GenParticles.

It is also true that this code is currently used by default in PAT but this will change soon. Nevertheless, for backward compatibility or to be able to reproduce old results, it's good to keep the old flavor code available as an optional feature in the PAT workflow.