All, this is a bug (or unsupported) in twitter’s API. There is a point in most people’s favorites history that the API just stops returning results. Often you can see the same “missing” favorites on the actual favorite list on Twitter.com. I hope to find a resolution, but we are stuck with it for now.Ben commented
Just read this on the Twitter help page, which corresponds to the use of mass tweet deletion programs: https://support.twitter.com/groups/55-troubleshooting/topics/231-tweets-direct-messages/articles/277671-i-m-missing-tweets. I suspect the same applies to mass unfavouriting
They appear to be working on a solution to restore truncated profiles due to mass tweet deletion (where a certain number of tweets are indicated, but non displayed). Hopefully, this means truncated favourite lists - such as mine http://twitter.com/@_bensalt - will also be restored.