If you have the fonts used in the document on your system, unembed the fonts using the PDF Optimizer and use the Print Production tool to re-embed all of the fonts. What you see happens frequently due to font subsetting. If the entire fonts is embedded into the doucment it won't happen.
I got it figured out another way. When combining single files into one file, choose the small file size in the option button. All letters & numbers kept their formatting that way.
Thanks for the help.
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