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MyClipping.txt is just a dumb log that records note-taking UI events.
The reading software reads and uses notes & highlights stored inside a (binary, non "plaintext) file that is / was inside book related ".sdr" folder, doesn't care about MyClipping.txt contents. When you deleted that book using Calibre it also deleted associated ".sdr" folder so that data is now lost.
In short, there is nothing you can do (other than maaaaybe try using some kind of "undelete" / "restore deleted files" typed of program [like "Recuva" for Windows OS] to scan Kindle drive on your computer and to check if that deleted data hadn't been overwritten already and restore it).
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