The My Clippings.txt actually has little to do with what annotations are shown in the book. It is really just a log of the annotations you have made over time. Each time you make an annotation, it is added to the end of the My Clippings.txt file and never used again. The annotation you see when reading are stored elsewhere. As you add or remove the annotations, they are added and removed from that location
I'm not sure where the annotations are actually stored. My memory suggests a file with the extension .sbr alongside the book. But, a quick search doesn't find any prove. It might be in a database somewhere hidden from view.
Because of this, I believe the connection between the annotations and book can get lost if the file name of the book changes. If you resend the book with a different file name, then the device won't be able to connect the store annotations to the actual book. And if something in the book is changed, it's possible the annotations will still be there, but, cannot be displayed when reading. They might be in an annotations list (I assume the Kindle has one), but, not visible elsewhere.
Note: My actual Kindle experience is limited to playing with them in a shop. Everything else is based on comments here and the work done maintaining the Annotations plugin.
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