This is a query, to which I don't think there is a solution.

If I have (say) 100 html files, I can use Coffee Cup Editor to do a global replace on each one, ok so far.

But if I want to insert the number '1' into one html file and the number '2' into the next one and so on until I get to the hundredth one and insert '100' into this one, I don't think I can do this by any other means, other than edit each one in turn - is this correct?

Yes, that is correct.