This symptom is caused by a problem with fonts: When you combine two files that use two different subsets of the same font, and there is a problem with how these two subsets were created, Acrobat has to assume that both subsets are identical, so it's not combining the two subsets, and you will be missing the characters that are either not in the first or not in the second document.
This should however not happen when the source files were created with Acrobat.
Would you be able to share two of these source files with me that show this problem when merged?
Karl Heinz Kremer
PDF Acrobatics Without a Net
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