Running on Structural Different root files

Hi Rooters,
I’m trying to run my code on a set of root files, but their structures are not identical.
(This is because LHC is producing more and more data now and the previous root files are slimed with new coming data.)
One might think of running the files separately and then merge the outputs afterwards. But I’m analyzing data iteratively, each iteration depends on the information get from the previous one, so It’s difficult to split the dataset.
I tried to run together, but it turned out the program stops at some point, less than 10% of the whole dataset.
Maybe I couldn’t do it like this?

Thank you very much.

We cannot do much with what you say. Could you provide the shortest possible setup and data set reproducing your problem?