I keep wondering if you could use an SQLite database (file...) here. Kind of like a tied-hash only better. I do not know how many elements in these massive files actually change from one run to the next; nor how many are in common. But maybe you could capture data from first one then the other into an SQLite table, which, since it is just a file, requires no server setup. Determine what differences actually exist, then use these to update or to rebuild file C.
The overall strategy of using two massive XML files needs to be reviewed carefully, either by you or by your managers or both.
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