Multiple Copies/Versions of a Book

Ok, I am very likely over thinking this.
I have a number of books that hit one of these situations:
1. I bought a book that is part of a series. I then later bought an omnibus which included the book I already own.
2. I have an updated version of a book which was expanded.
3. The eBook includes as sample of another book at the end. I want to remove the sample from the version I use but keep the original ePub in case I want read the sample. (I am planning to use the ePub splitter plugin, unless someone has a better suggestion)

For some reason, I want to keep the meta-data in the first two cases. However, I want to effectively "hide" the book from my regular catalog, by somehow making it an alternate version of the Omnibus, or some sort of archive.

For the third case, I think those I can keep as additional ePub files, but I have not figured out how that works.

Any suggestions on some feature of Calibre and Kobo that I am overlooking or how to handle these use cases?

Tim