The "My Clippings" file is only a log (record) that highlights and notes have been made. Kindles only ever write to it, never read from it.
Highlights, notes, etc are stored in the .sdr directory for the book. If you want to preserve them, you need to backup the contents of the .sdr directory.
For details regarding these files. see:
https://www.mobileread.com/forums/sh...d.php?t=321811
https://www.mobileread.com/forums/sh...d.php?t=322172