At this point I am at a loss. It can't be that the plugin simply doesn't work on Linux; we would have been told that by now. That says that something is odd about your installation.
These books seem to be out of copyright. Can you either send me a copy of the ones that are breaking, especially one where it removes the entries from the ncx? Send them to modepub [at] charleshaley [dot] org. I don't have a linux machine but I might be able to see something.
More questions:
- You are accepting the changes when the plugin finishes?
- Are you sure the files are being written back to the library? Please note the mod time, run the plugin, then check that the time and size changed.
- Check the permissions on the book to be sure that calibre has write permission on the directory.
- Are you using "normal" Linux file systems to store the library? Not a NAS, not an external drive?