Hi Amin,
The message indicates that the files you are using have been written with different schema for the class MissingET and that when the change was made, the author ‘forgot’ to increase the version number. Because of this you might not be able to read those files in the same ROOT session and may not be able to merge them. (If I interpreter correctly the message some files have MissingET::Eta and some do not, ROOT can not guess what should be the value to use when it is missing).
Similarly the files seems to have various schema for the class Jet leading to similar problem.
Note: did you try using the ‘hadd’ utility rather than adapting copytree3.C? In particular it would default to using the fast cloning mode (i.e. be faster) which would also likely solve the problem for Jet.
Cheers,
Philippe.