Hi @ramkrishna ,
you cannot use a header obtained by running MakeClass on a given TTree to process another TTree with a different schema (e.g. less branches). You should at least modify the code so that it does not call SetBranchAddress for the missing branches.
I am not sure what you mean, two entries where? In the ROOT file? You might just be seeing namecycles: you can safely ignore the repeated entries if they are of the form treename;1 and treename;2 – the short version is that data is saved to file only once, those are two versions of the metadata, and ROOT automatically only considers the latest. It’s a data-loss-prevention mechanism.
Cheers,
Enrico