'My Clippings.txt' is a log file that records each bookmark, note, or highlight you create on your Kindle (regardless of whether it was from Amazon). If you delete a note or highlight, no record is made of such a deletion. If you remove an annotated item, the log record of the annotation remains. If you modify a note, it will still have a record of the original note. So the point is that My Clippings is a historical record, not a snapshot of the current state of notes, highlights, and bookmarks.
Highlights, notes and bookmarks created for books linked to your Amazon account are saved with your account and can be viewed on any Kindle or Kindle app linked to it. But only the device/app where the note was created will have a record in the 'My Clippings.txt' file (and if the clippings file is deleted for whatever reason, not even then).
It would be nice if Kindle had an 'export' feature that let you generate a text file with a 'snapshot' of all of the annotations, bookmarks, and highlights that exist on that device at the time. As it is there's not always an easy way to extract notes/highlights for re-use on a computer, etc., apart from going to each item, viewing 'my notes and marks' and taking screenshots, etc. I'll be sending this suggestion to email@example.com