I used to do it the same way: open "Notes" window on Kindle, open epub file (since I use epubs as "master copy" in my Calibre library) with Calibre Editor (used to be Sigil instead of Calibre Editor) on PC, fix a problem> delete the note from Kindle Notes section. Once I'm finished I re-convert epub to azw3 for the future (probably newer to happen) re-reads.
Yeah, MyClippings.txt is just a dumb event log for events regarding bookmarking and note-taking activities. That chronicles just the adding part not the removing. So I end up with 95% of MyClippings.txt records being about long gone bookmark markers (since I tend to use bookmarks every time I stop reading, just in case someone else picks up my Kindle and starts to swype away forwards/backwards ... which does happen especially when young children come to visit
, if I fail to promptly hide away my most precious gadget).
Kindle OS itself reads the necessary up-to-date information (once you open the book ) from those "sidecar" files I've mentioned previously.