Is there any way to use Yahoo Pipes to remove RSS feed items that are covering the same news story?

Pipes offers a "Unique" module but it requires that you identify the fields that uniquely identify an item in the feed.

For your particular problem Yahoo Pipes might not be a complete solution, as building more complex filtering logic in Pipes is quite difficult, if not impossible. I have a option, but it is non-trivial.  Consider https://github.com/ggaughan/pipe2py it's a program that will download and convert your Pipe logic into Python So you could have Yahoo Pipe setup with all the logic you expect you need for the aggregation of your input feeds.  Insert a "null operation" of some sort before the output of your stream, look for that operation in the python output program. Create a filter module and replace the null operation with your filter, and run the subsequent python program, (perhaps on a cron job, that outputs an rss file to a local webserver?  I'm not sure about that last mile bit) Using your already existing Pipe logic to bootstrap your own filter that you could get running on Google AppEngine. But be aware that neither Yahoo or the output Python program would have knowledge of articles in the past - only their current window of feeds - if a new article pops up days later than the rest of the pack, you'll probably still see it. Good luck. Yahoo Pipes is a great tool, but is limited in scope as to what it can do, also look into YQL, I don't think it will help you in your current endeavor, but its a good tool to know well.

Do not use Yahoo Pipes full stop period! A few years ago a build a set of Yahoo Pipes interfaces that I figured were pretty cool, they were deprecated without much notice.  They are a waste of effort.