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Maybe you could provide more information about the type of replacement you need to do.
Generally, if a pattern might take place across two or more lines, you build up the lines in the Hold space with the H command, or use `N' to build up the lines in the pattern space. Once you have a group of lines in the Hold space you need, you can get them (or exchange them) to the pattern space. At this point a substitute command can use `\n' in the RHS pattern. Bear in mind, that you now have to consider patterns that include newlines. You may need to use braces to group commands to run after building up the lines in the pattern space if you need to deal with more than one type of pattern.
Your problem may not be that the pattern to replace is across several lines or the entire file, but that you want to process lines that are in a range of lines, based on a pattern.