Are you looking for an exact paragraph match (eg exact spaces, punctuation, and newlines)?

Yes. Basically I'm writing configuration paragraphs into configuration files.

The problem with an exact match is that two configuration paragraphs may be semantically equivalent, but syntactically different, e.g. in a different order, or with different whitespace. It seems, to me, that the only foolproof way to avoid duplicates would be an actual parser for the config files. Unless you can ensure that semantically equal paragraphs will be syntactically identical, you might be creating duplicates. And with a lot of files, as you say you have, this would make cleaning up any mistakes just as hard.

Just something to think about...