I would tend to do it the other way around: store the waivers into a hash (a simple hash) where the key is the common identifier between the two files, and then read the violations file line by line, changing the content of the line when the identifier is common between the two files and writing the line to the new files. This is often more efficient this way.

But since we don't know about the size of the violations and waivers files, it actually may be that your solution is better (especially if there are many more waivers than violations, but that's seems rather unlikely).