FYI,
I've posted a test version of EpubMerge that may be of interest to greeniron and other users who want a better way to deal with anthologies of stories.
It contains a feature to allow merged epubs to automatically be UnMerged to their original epubs again. These can then be updated with FFDL before merging back together again. It's still a several step process, but it's an improvement.
https://www.mobileread.com/forums/sho...08#post2418308
I have plans to integrate this with FFDL for a better user experience, but this is the first step.