I created a mobi file, and uploaded to my android phone via usb connection, read it in the "Kindle for Android" app and made some notes and highlights. Kindle App seemingly stored them in the .embp file sitting next to the .mobi file. Is there any way I could now view those highlights and notes on my PC?
It seems like since the Kindle for Android version 188.8.131.52, Amazon started to encrypt the mbp files and apparently no software can read it, unfortunately.
One workaround you can try to do is to uninstall all the updates of the Kindle app down to at least version 184.108.40.206, so that you get your notes back in the .mbp format, which in turn can be read by the application called "MBP Reader" (Win/Linux), made by someone who managed to reverse-engineer the MBP format. It is available for download here.
Hope that helps.