(I'm assuming here that you don't have direct access to what the changed section looked like before: if you did, diffing that to the new version with plenty of context and applying it with patch is trivial.) If you can identify with certainty which part of the big file is the changed section, you can replace it with their changes. If you can't identify it with certainty, there isn't anything I see that will solve the problem for you unambiguously.
I think you are going to have to show what this data looks like to get help.