I have written some notes and highlighted some parts of one of my e-books on kindle. I can see those notes and highlights when I open the "My Clippings" file. But when I open the book, and try to see its notes and highlights via "Menu > View Notes & Marks", nothing is shown. I think this happened after I deregistered UserA, registered UserB, deregisterd UserB and registered UserA again. How can I see my notes when I am reading the book?
When you make a highlight or note, a copy is written to the My Clippings file. This is a one-time, one-way operation. Think of it as a record of the notes and highlights that you've made in the past. The file is only a text file, and you can open it on your computer and modify it any way you like, or even delete it, and it will have no effect on what you see when you read the book on your Kindle. Likewise, removing or changing a highlight or note in the Kindle book will not affect the original entry in My Clippings, although it may create a new entry.
The notes and highlights that are displayed in Kindle books are stored in a companion file on the Kindle. It used to have a .mbp suffix, but it may be different with the newer formats. What may have happened in your case is that you downloaded the book file but not the companion file. This can happen if you downloaded it to your computer and transfered to the Kindle with a USB cable, or if you just did not allow enough time for all the "extras" to be downloaded before turning off wireless.
One more possibility is that you deleted the book and/or deregistered it from the original account before the Kindle was able to back them up on Amazon's servers. Normally this happens in the background, but if you do not use wireless very often, it may not have happened. If that is the case, your notes may actually be gone, but as Debra said, you do at least still have the copy in the My Clippings file, and that can also be your guide if you want to put them back in the book as well.
I suspect that the deregistering and re-registering may have lost the connection between that book and your "My Clippings" file. If you have allowed Amazon to synch your highlights and bookmarks, you may be able to remove the book from your kindle and then re-download it from Amazon. That ought to re-load the bookmarks.
You might also try creating a new, short note in the same place as a previous note. But that's a long shot .... You might have lost the highlights within that book. You can, of course, connect the Kindle to your computer with a USB cable and copy off that "My Clippings" file, and save the highlights that are in there. That wouldn't get them into the book, but you would at least save your typing effort.