MyClippings.txt file is just a simple historical log file of events that get raised when user does something using the UI. It's one way, it doesn't "sync" ( = removing highlight in the UI doesn't remove already existing "record" from that file). So you can't expect it to "repopulate" clippings file from old notes stored in SDR folder. Only new bookmark / highlight / note that you were to create now would get written into clippings file (if you Kindle still uses firmware file that still creates it, since IIRC that was recently removed?).
As for extracting the text you highlighted and notes text your best bet would probably be to ask very nicely the developer of that Kindle Reader Dashboard plugin to add export functionality.
Of that's not an option you will probably need at least some basic knowledge of programming & scripting to do the extraction yourself. Either by snooping around and figuring out how (maybe inside a SQLite database?) that plugin stores the notes it imported and writing the code to extract the information yourself.
Or alternatively try and use multiple existing scripts to do the job. IIRC you would need to use
this to decode information stored in SDR folder into JSON output and then use
another script written by @j.p.s to extract the actual highlighted text based on offsets in that previous JSON output?