Page numbering changes formatting of legal documents

I have seen in the past that my court documents do not come the same as when I make them. I finally narrowed the issue. First, I am working with a PDF document created by combining multiple files. Some of those files are of a legal format with the line numbers on the left side and doble line separateing those line numbers form the rest of the text. Once I am executing page numbering command in Adobe Pro - this command also removes the line numbers and double lines from some of the included documents. I cannot epxress my frustratoin to see that the documents on which I spend hours on formatting were filed in this unconfirming format.