Hi Delo,
Indeed if you update the ROOT file (well any file) there is a risk that if something goes wrong (physical error in the hard drive, random crash due to any problem in your code or the library you use), the result would be a corrupted file.
The only safe solution (short of never having bug in your code or never tickling bug in the library code 
) is to make a backup copy of the file. You can for example using the shell command cp or even TFile::Cp to make the copy or you could open the file read only and copy the content into a new file. For example:TFile *f1 = TFile::Open("zjet2DBS_15to20.root","READ");
TTree *tree = 0;
f1->GetObject("myEvent",tree);
TFile *output = TFile::Open("zjet2DBS_15to20_v2.root","NEW");
TTree *newtree = tree->CloneTree(-1,"fast");
newtree->SetWeight(0.4);
output->Write();
delete f1;
delete output;
Cheers,
Philippe.