Actually, Olivier hasn’t missed your previous question - he wrote:
Also, I suggest you post your full script here. How are you applying your cuts? Are you working with SetBranchAddress? Maybe there is some bug in your script causing undefined behavior and thus leading to a root file broken in a “funny” way?
If you are just applying simple cuts, you could also try to use CopyTree instead of CloneTree, for example:
auto treeWithCutsApplied = sourceTree->CopyTree("answer > 42");